Compositions and methods for treating cancer

ABSTRACT

K-Ras is the most frequently mutated oncogene in human cancer. Disclosed herein are compositions and methods for modulating K-Ras and treating cancer.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.16/013,271 filed Jun. 20, 2018, which is a continuation of U.S.application Ser. No. 14/934,184 filed Nov. 6, 2015, issued as U.S. Pat.No. 10,023,588, which is a continuation of U.S. application Ser. No.14/391,369 filed Oct. 8, 2014, abandoned, which is a Section 371 ofPCT/US2013/036031 filed Apr. 10, 2013, which claims priority to U.S.Application No. 61/622,507 filed Apr. 10, 2012; U.S. Application No.61/728,145 filed Nov. 19, 2012; and U.S. Application No. 61/794,956filed Mar. 15, 2013, which are all incorporated herein by reference intheir entirety and for all purposes.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAMLISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE

The Sequence Listing written in file 048536-527C03US_ST25.TXT, createdon Dec. 18, 2019, 28,747 bytes, machine format IBM-PC, MS-Windowsoperating system, is hereby incorporated by reference.

BACKGROUND OF THE INVENTION

K-Ras is the most frequently mutated oncogene in human cancer. However,past attempts to directly target this enzyme with reversible inhibitorshave been almost entirely unsuccessful.

Ras proteins are small guanine nucleotide-binding proteins that act asmolecular switches by cycling between active GTP-bound and inactiveGDP-bound conformations. Ras signaling is regulated through a balancebetween activation by guanine nucleotide exchange factors (GEFs), mostcommonly son of sevenless (SOS), and inactivation by GTPase-activatingproteins (GAPs) such as neurofibromin or p120GAP (see FIG. 1). The Rasproteins play a critical role in the regulation of cell proliferation,differentiation, and survival. Dysregulation of the Ras signalingpathway is almost invariably associated with disease. Hyper-activatingsomatic mutations in Ras are among the most common lesions found inhuman cancer. Most of these mutations have been shown to decrease thesensitivity of Ras to GAP stimulation and decrease its intrinsic GTPaseactivity, leading to an increase in the active GTP-bound population.Although mutation of any one of the three Ras isoforms (K-Ras, N-Ras, orH-Ras) has been shown to lead to oncogenic transformation, K-Rasmutations are by far the most common in human cancer. For example, K-Rasmutations are known to be often associated with pancreatic, colorectaland non-small-cell lung carcinomas. Similarly, H-Ras mutations arecommon in cancers such as papillary thyroid cancer, lung cancers andskin cancers. Finally, N-Ras mutations occur frequently inhepatocellular carcinoma.

The structural basis for the Ras cycle and Ras hyperactivation are wellunderstood. Over 40 crystal structures of H-Ras have been solved,including both wild-type and mutants bound to GDP or analogs of GTP.Likewise, the structures of H-Ras in complex with many of its bindingpartners are known. The nucleotide-binding pocket is bordered by fourmain regions: the phosphate-binding loop (P-loop, residues 10-17),Switch 1 (residues 30-40), Switch 2 (residues 60-76), and thebase-binding loops (residues 116-120 and 145-147), (Hall et al. PNAS,2002, 19, 12138-12142 and Vetter 2001 Science). The Switch regionsgovern interactions between Ras and its binding partners by adoptingdifferent conformations when bound to GTP or GDP. Threonine-35 andglycine-60 make key hydrogen bonds with the γ-phosphate of GTP, holdingthe Switch 1 and Switch 2 regions in the active conformation,respectively. Upon hydrolysis of GTP and release of phosphate, these tworegions are free to relax into the inactive GDP conformation.

The regions bordering the nucleotide pocket also contain the most commonsites of Ras mutation in cancer. The vast majority of oncogenicmutations occur at residues 12 or 13 in the P-loop, or residue 61 inSwitch 2. Structural data suggest that mutation of glycine-12 orglycine-13 would sterically occlude the critical arginine residue of theGAP and thus prohibit inactivation of Ras signaling. Mutation ofglutamine-61 similarly impairs GAP-mediated Ras inactivation.

Thus, there is a need in the art for effective Ras inhibitors andanticancer compounds. The present invention provides solutions to theseand other problems in the art.

BRIEF SUMMARY OF THE INVENTION

Described herein, inter alia, is the use of covalent (e.g. reversible orirreversible) chemistry to target a Ras protein, including but notlimited to chemically tractable oncogenic mutants such as K-RasG12C.Also described herein, inter alia, are the first small molecules whichspecifically target the human oncogene (K-RasG12C) and do not bind tothe proto-oncogenic form of the protein (K-Ras).

In a first aspect, a compound having the formula R¹-L¹-L²-L³-E isprovided. R¹ is a Switch 2—Binding Pocket binding moiety. L¹ is a bondor a divalent radical chemical linker. L² is a bond or a divalentradical chemical linker. L³ is a bond or a divalent radical chemicallinker. E is an electrophilic chemical moiety capable of forming acovalent bond with a Ras (e.g. K-Ras) cysteine residue or a Ras (e.g.K-Ras) aspartate residue.

In a second aspect, a pharmaceutical composition including apharmaceutically acceptable excipient and a compound described herein(including embodiments, examples, and in Table 1, 2, 3, 4, or 5) isprovided.

In a third aspect, a method of treating a disease in a patient in needof such treatment is provided. The method including administering atherapeutically effective amount of a compound described herein(including embodiments, examples, and in Table 1, 2, 3, 4, or 5) to thepatient.

In a fourth aspect, a method of modulating the activity of a K-Rasprotein is provided. The method including contacting the K-Ras proteinwith an effective amount of a compound described herein (includingembodiments, examples, and in Table 1, 2, 3, 4, or 5).

In a fifth aspect, a method of modulating a K-Ras protein is provided.The method including contacting the K-Ras protein with an effectiveamount of a compound described herein (including embodiments, examples,and in Table 1, 2, 3, 4, or 5).

In a sixth aspect, a K-Ras protein covalently bonded to a compound, suchas, for example, a compound described herein (including modulators,inhibitors, embodiments, examples, and in Table 1, 2, 3, 4, or 5) isprovided. The compound is covalently bonded to a cysteine residue of theK-Ras protein.

In a seventh aspect, a K-Ras protein covalently bonded to a compound,such as, for example, a compound described herein ((includingmodulators, inhibitors, embodiments, examples, and in Table 1, 2, 3, 4,or 5) is provided. The compound is covalently bonded to an aspartateresidue of the K-Ras protein.

In an eighth aspect, a method of identifying a covalent inhibitor ofK-Ras protein is provided. The method including contacting a K-Rasprotein with a K-Ras inhibitor test compound, allowing the K-Rasinhibitor test compound to covalently inhibit the K-Ras protein, anddetecting the level of covalent inhibition of the K-Ras protein, therebyidentifying a covalent inhibitor of K-Ras protein.

In some embodiments, provided is a compound having the formula:R¹-L¹-L²-L³-Ewherein, R¹ is a Switch 2—Binding Pocket binding moiety; L¹ is a bond ora divalent radical chemical linker; L² is a bond or a divalent radicalchemical linker; L³ is a bond or a divalent radical chemical linker; andE is an electrophilic chemical moiety capable of forming a covalent bondwith a K-Ras cysteine residue or a K-Ras aspartate residue. In someembodiments, R¹ is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Forexample, R¹ is substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; or R¹ is substituted orunsubstituted aryl or substituted or unsubstituted heteroaryl, such assubstituted or unsubstituted fused ring aryl or substituted orunsubstituted fused ring heteroaryl. In some embodiments, R¹ isR³-substituted or unsubstituted aryl or R³-substituted or unsubstitutedheteroaryl, wherein R³ is independently hydrogen, oxo, halogen, —CX₃,—CN, —SO₂Cl, —SO_(n)R¹, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂,—NHC═(O)NR⁷R⁸, —N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸, —OR¹⁰,—NR⁷SO₂R¹⁰, —NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; two adjacent R³ substituentsmay optionally be joined to form a substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. TwoR³ substituents bonded to the same atom may optionally be joined to forma substituted or unsubstituted cycloalkyl or substituted orunsubstituted heterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independentlyhydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH,—SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R⁷ and R⁸ substituents bondedto the same nitrogen atom may optionally be joined to form a substitutedor unsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; m and v are independently 1 or 2; n is independently aninteger from 0 to 4; and X is independently —Cl, —Br, —I, or —F.

In some embodiments, R¹ is:

wherein, R³ is independently hydrogen, oxo, halogen, —CX₃, —CN, —SO₂Cl,—SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸,—N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰,—NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; two adjacent R³ substituents may optionally bejoined to form a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; two R³ substituents bonded tothe same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R⁷ and R⁸ substituents bonded to the samenitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; m and v are independently 1 or 2; n is independently aninteger from 0 to 4; X is independently —Cl, —Br, —I, or —F; e2 isindependently an integer from 0 to 2; e3 is independently an integerfrom 0 to 3; e4 is independently an integer from 0 to 4; e5 isindependently an integer from 0 to 5; e6 is independently an integerfrom 0 to 6; and e7 is independently an integer from 0 to 7.

In some embodiments, R¹ is R³-substituted pyridinyl, R³-substitutedpyrimidinyl, R³-substituted thiophenyl, R³-substituted furanyl,R³-substituted indolyl, R³-substituted benzoxadiazolyl, R³-substitutedbenzodioxolyl, R³-substituted benzodioxanyl, R³-substitutedthianaphthanyl, R³-substituted pyrrolopyridinyl, R³-substitutedindazolyl, R³-substituted quinolinyl, R³-substituted quinoxalinyl,R³-substituted pyridopyrazinyl, R³-substituted quinazolinonyl,R³-substituted benzoisoxazolyl, R³-substituted imidazopyridinyl,R³-substituted benzofuranyl, R³-substituted benzothiophenyl,R³-substituted phenyl, R³-substituted naphthyl, R³-substituted biphenyl,R³-substituted pyrrolyl, R³-substituted pyrazolyl, R³-substitutedimidazolyl, R³-substituted pyrazinyl, R³-substituted oxazolyl,R³-substituted isoxazolyl, R³-substituted thiazolyl, R³-substitutedfurylthienyl, R³-substituted pyridyl, R³-substituted pyrimidyl,R³-substituted benzothiazolyl, R³-substituted purinyl, R³-substitutedbenzimidazolyl, R³-substituted isoquinolyl, R³-substituted thiadiazolyl,R³-substituted oxadiazolyl, R³-substituted pyrrolyl, R³-substituteddiazolyl, R³-substituted triazolyl, R³-substituted tetrazolyl,R³-substituted benzothiadiazolyl, R³-substituted isothiazolyl,R³-substituted pyrazolopyrimidinyl, R³-substituted pyrrolopyrimidinyl,R³-substituted benzotriazolyl, or R³-substituted quinolyl; where R³ isindependently hydrogen, oxo, halogen, —CX₃, —CN, —SO₂Cl, —SO_(n)R¹,—SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂, —NHC ═(O)NR⁷R⁸, —N(O)_(m),—NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰, —NR⁷C═(O) R⁹,—NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; two adjacent R³ substituents may optionally be joined toform a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; two R³ substituents bonded tothe same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R⁷ and R⁸ substituents bonded to the samenitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; m and v are independently 1 or 2; n is independently aninteger from 0 to 4; and X is independently —Cl, —Br, —I, or —F.

In other embodiments, R¹ is unsubstituted pyridinyl, unsubstitutedpyrimidinyl, unsubstituted thiophenyl, unsubstituted furanyl,unsubstituted indolyl, unsubstituted benzoxadiazolyl, unsubstitutedbenzodioxolyl, unsubstituted benzodioxanyl, unsubstitutedthianaphthanyl, unsubstituted pyrrolopyridinyl, unsubstituted indazolyl,unsubstituted quinolinyl, unsubstituted quinoxalinyl, unsubstitutedpyridopyrazinyl, unsubstituted quinazolinonyl, unsubstitutedbenzoisoxazolyl, unsubstituted imidazopyridinyl, unsubstitutedbenzofuranyl, unsubstituted benzothiophenyl, unsubstituted phenyl,unsubstituted naphthyl, unsubstituted biphenyl, unsubstituted pyrrolyl,unsubstituted pyrazolyl, unsubstituted imidazolyl, unsubstitutedpyrazinyl, unsubstituted oxazolyl, unsubstituted isoxazolyl,unsubstituted thiazolyl, unsubstituted furylthienyl, unsubstitutedpyridyl, unsubstituted pyrimidyl, unsubstituted benzothiazolyl,unsubstituted purinyl, unsubstituted benzimidazolyl, unsubstitutedisoquinolyl, unsubstituted thiadiazolyl, unsubstituted oxadiazolyl,unsubstituted pyrrolyl, unsubstituted diazolyl, unsubstituted triazolyl,unsubstituted tetrazolyl, unsubstituted benzothiadiazolyl, unsubstitutedisothiazolyl, unsubstituted pyrazolopyrimidinyl, unsubstitutedpyrrolopyrimidinyl, unsubstituted benzotriazolyl, or unsubstitutedquinolyl.

In some embodiments, L¹, L² and L³ are independently a bond, —NR^(2C)—,—O—, —S—, —C(O)—, —S(O)—, —S(O)₂—, substituted or unsubstitutedalkylene, substituted or unsubstituted heteroalkylene, substituted orunsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, substitutedor unsubstituted heteroarylene; or a substituted or unsubstitutedspirocyclic linker; R^(2C) is independently hydrogen, oxo, halogen,—CX^(c) ₃, —CN, —SO₂Cl, —SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c), —NHNH₂,—ONR⁷CR^(8c), —NHC═(O)NHNH₂, —NHC═(O)NR^(7c)R^(8c), —N(O)_(m3),—NR^(7c)R^(8c), —C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c),—OR^(10c), —NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c),—NR^(7c)C(O)—OR^(9c), —NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; Two adjacent R^(2C)substituents may optionally be joined to form a substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; Two R^(2C) substituents bonded to the same atom mayoptionally be joined to form a substituted or unsubstituted cycloalkylor substituted or unsubstituted heterocycloalkyl; R^(7c), R^(8c), R^(9c)and R^(10c) are independently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R^(7c)and R^(8c) substituents bonded to the same nitrogen atom may optionallybe joined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; m1, m3, v1, and v3 areindependently an integer from 1 to 2; n1 and n3 are independently aninteger from 0 to 4; and X^(c) is independently —Cl, —Br, —I, or —F.

In some embodiments, L¹, L² and L³ are independently —CR^(2A)R^(2B)—,

R^(2A) and R^(2B) are independently hydrogen, oxo, halogen, —CX^(a) ₃,—CN, —SO₂Cl, —SO_(n1)R^(10a), —SO_(v1)NR^(7a)R^(8a), —NHNH₂,—ONR^(7a)R^(8a), —NHC═(O)NHNH₂, —NHC═(O)NR^(7a)R^(8a), —N(O)_(m1),—NR^(7a)R^(8a), —C(O)R^(9a), —C(O)—OR^(9a), —C(O)NR^(7a)R^(8a),—OR^(10a), —NR^(7a)SO₂R^(10a), —NR^(7a)C═(O)R^(9a),—NR^(7a)C(O)—OR^(9a), —NR^(7a)OR^(9a), —OCX^(a) ₃, —OCHX^(a) ₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R^(2A) and R^(2B) substituentbonded to the same atom may optionally be joined to form a substitutedor unsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R^(2C) is independently hydrogen, oxo, halogen,—CX^(c) ₃, —CN, —SO₂Cl, —SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c), —NHNH₂,—ONR^(7c)R^(8c), —NHC═(O)NHNH₂, —NHC═(O)NR^(7c)R^(8c), —N(O)_(m3),—NR^(7c)R^(8c), —C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c),—OR^(10c), —NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c), —NR^(7c)(O)—OR^(9c),—NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(7a), R^(8a), R^(9a) and R^(10a) are independentlyhydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH,—SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R^(7a) and R^(8a) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; R^(7c), R^(8c), R^(9c) and R^(10c) areindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R^(7c) and R^(8c) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; z is independently an integer from 0 to 10;m1, m3, v1, and v3 are independently an integer from 1 to 2; n1 and n3are independently an integer from 0 to 4; and X^(a) and X^(c) areindependently —Cl, —Br, —I, or —F.

In some embodiments, L¹ is independently substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, substituted or unsubstitutedheteroarylene, or substituted or unsubstituted spirocyclic linker; or L²is independently substituted or unsubstituted cycloalkylene, substitutedor unsubstituted heterocycloalkylene, substituted or unsubstitutedarylene, substituted or unsubstituted heteroarylene, or substituted orunsubstituted spirocyclic linker; or L³ is independently substituted orunsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, substitutedor unsubstituted heteroarylene, or substituted or unsubstitutedspirocyclic linker. In some embodiments, L¹ is independentlyR^(2C)-substituted or unsubstituted cycloalkylene, R^(2C)-substituted orunsubstituted heterocycloalkylene, R^(2C)-substituted or unsubstitutedarylene, R^(2C)-substituted or unsubstituted heteroarylene, orR^(2C)-substituted or unsubstituted spirocyclic linker; or L² isindependently R^(2C)-substituted or unsubstituted cycloalkylene,R^(2C)-substituted or unsubstituted heterocycloalkylene,R^(2C)-substituted or unsubstituted arylene, R^(2C)-substituted orunsubstituted heteroarylene, or R^(2C)-substituted or unsubstitutedspirocyclic linker; or L³ is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C)-substituted or unsubstituted heteroarylene, or R^(2C)-substitutedor unsubstituted spirocyclic linker.

In some embodiments, L¹ is independently

L² is independently

L³ is independently

andwherein f2 is independently an integer from 0 to 2; f6 is independentlyan integer from 0 to 6; f7 is independently an integer from 0 to 7; f8is independently an integer from 0 to 8; f9 is independently an integerfrom 0 to 9; f10 is independently an integer from 0 to 10; f12 isindependently an integer from 0 to 12; f14 is independently an integerfrom 0 to 14.

In some embodiments, E comprises

wherein R¹³ is independently hydrogen, oxo, halogen, —CX^(b) ₃, —CN,—SO₂Cl, —SO_(r)R¹⁷, —SO_(p)NR¹⁴R¹⁵, —NHNH₂, —ONR¹⁴R¹⁵, —NHC═(O)NHNH₂,—NHC═(O)NR¹⁴R¹⁵, —N(O)_(q), —NR¹⁴R¹⁵, —C(O)R¹⁶, —C(O)—OR¹⁶,—C(O)NR¹⁴R¹⁵, —OR¹⁷, —NR¹⁴SO₂R¹⁷, —NR¹⁴C═(O)R¹⁶, —NR¹⁴C(O)OR¹⁶,—NR¹⁴OR¹⁶, —OCX^(b) ₃, —OCHX^(b) ₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl; twoadjacent R¹³ substituents may optionally be joined to form a substitutedor unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; Two R¹³ substituents bonded to the same atommay optionally be joined to form a substituted or unsubstitutedcycloalkyl or substituted or unsubstituted heterocycloalkyl; R¹⁴, R¹⁵,R¹⁶, and R¹⁷ are independently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R¹⁴ andR¹⁵ substituents bonded to the same nitrogen atom may optionally bejoined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; p is independently 1 or 2; q isindependently an integer from 1 to 2; r is independently an integer from0 to 4; and X^(b) is independently —Cl, —Br, —I, or —F.

In some embodiments, E may comprise a substituted or unsubstituted vinylsulfone moiety, substituted or unsubstituted vinyl sulfonamide moiety,substituted or unsubstituted fluoro(C₁-C₄)alkylketone moiety,substituted or unsubstituted chloro(C₁-C₄)alkylketone moiety,substituted or unsubstituted acrylamide moiety, substituted orunsubstituted disulfide moiety, substituted or unsubstituted thiolmoiety, substituted or unsubstituted phosphonate moiety, substituted orunsubstituted aldehyde moiety, substituted or unsubstituted enonemoiety, substituted or unsubstituted diazomethylketone moiety,substituted or unsubstituted diazomethylamide moiety, substituted orunsubstituted cyanocyclopropyl carboxamide moiety, substituted orunsubstituted epoxide moiety, substituted or unsubstituted epoxyketonemoiety, substituted or unsubstituted epoxyamide moiety, substituted orunsubstituted aryl aldehyde moiety, substituted or unsubstituted aryldialdehyde moiety, substituted or unsubstituted dialdehyde moiety,substituted or unsubstituted nitrogen mustard moiety, substituted orunsubstituted propargyl moiety, substituted or unsubstitutedpropargylamide moiety.

In some embodiments, E comprises an unsubstituted vinyl sulfone moiety,unsubstituted vinyl sulfonamide moiety, unsubstitutedfluoro(C₁-C₄)alkylketone moiety, unsubstituted chloro(C₁-C₄)alkylketonemoiety, unsubstituted acrylamide moiety, unsubstituted disulfide moiety,unsubstituted thiol moiety, unsubstituted phosphonate moiety,unsubstituted aldehyde moiety, unsubstituted enone moiety, unsubstituteddiazomethylketone moiety, unsubstituted diazomethylamide moiety,unsubstituted cyanocyclopropyl carboxamide moiety, unsubstituted epoxidemoiety, unsubstituted epoxyketone moiety, unsubstituted epoxyamidemoiety, unsubstituted aryl aldehyde moiety, unsubstituted aryldialdehyde moiety, unsubstituted dialdehyde moiety, unsubstitutednitrogen mustard moiety, unsubstituted propargyl moiety, orunsubstituted propargylamide moiety.

In some embodiments, the compound is a compound of Formula:

or a pharmaceutically acceptable salt thereof, wherein: e5 is an integerfrom 0 to 5; X′ is —O—, —NH—, or —S—; R^(2A) and R^(2B) areindependently hydrogen, substituted or unsubstituted alkyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R^(2A)and R^(2B) substituent bonded to the same atom may optionally be joinedto form a substituted or unsubstituted cycloalkyl or substituted orunsubstituted heterocycloalkyl; R³ is independently hydrogen, oxo,halogen, —CX₃, —CN, —SO₂Cl, —SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸,—NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸, —N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹,—C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰, —NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹,—OCX₃, —OCHX₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; L² isindependently R^(2C)-substituted or unsubstituted cycloalkylene,R^(2C)-substituted or unsubstituted heterocycloalkylene,R^(2C)-substituted or unsubstituted arylene, R^(2C)-substituted orunsubstituted heteroarylene, or R^(2C)-substituted or unsubstitutedspirocyclic linker; L³ is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C-)-substituted or unsubstituted heteroarylene, orR^(2C)-substituted or unsubstituted spirocyclic linker; E is anelectrophilic chemical moiety capable of forming a covalent bond with acysteine or aspartate residue; R^(2C) is independently hydrogen, oxo,halogen, —CX^(c) ₃, —CN, —SO₂Cl, —SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c),—NHNH₂, —ONR^(7c)R^(8c), —NHC═(O)NHNH₂, —NHC═(O)NR⁷CR⁸, —N(O)_(m3),—NR^(7c)R^(8c), —C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c),—OR^(10c), —NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c),—NR^(7c)C(O)—OR^(9c), —NR^(7c)OR^(9c), substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; two adjacent R^(2C) substituents may optionally be joined toform a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; two R^(2C) substituents bondedto the same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(7a), R^(8a), R^(9a) and R^(10a) are independentlyhydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH,—SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R^(7a) and R^(8a) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; R^(7c), R^(8c), R^(9c) and R^(10c) areindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; m, m1, m3, v, v1, and v3 areindependently 1 or 2; n, n1, and n3 are independently an integer from 0to 4; X, X^(a) and X^(c) are independently —Cl, —Br, —I, or —F.

In some embodiments, E comprises a substituted or unsubstituted vinylsulfone moiety, substituted or unsubstituted vinyl sulfonamide moiety,substituted or unsubstituted peroxide moiety, substituted orunsubstituted fluoro(C₁-C₄)alkylketone moiety, substituted orunsubstituted chloro(C₁-C₄)alkylketone moiety, substituted orunsubstituted acrylamide moiety, substituted or unsubstituted disulfidemoiety, substituted or unsubstituted thiol moiety, substituted orunsubstituted phosphonate moiety, substituted or unsubstituted aldehydemoiety, substituted or unsubstituted enone moiety, substituted orunsubstituted diazomethylketone moiety, substituted or unsubstituteddiazomethylamide moiety, substituted or unsubstituted cyanocyclopropylcarboxamide moiety, substituted or unsubstituted epoxide moiety,substituted or unsubstituted epoxyketone moiety, substituted orunsubstituted epoxyamide moiety, substituted or unsubstituted arylaldehyde moiety, substituted or unsubstituted aryl dialdehyde moiety,substituted or unsubstituted dialdehyde moiety, substituted orunsubstituted nitrogen mustard moiety, substituted or unsubstitutedpropargyl moiety, substituted or unsubstituted propargylamide moiety.

In some embodiments, L² is independently R^(2C)-substituted orunsubstituted heterocycloalkylene or R^(2C)-substituted or unsubstitutedspirocyclic linker and L³ is a bond. For example, L² is monocyclic 4, 5,or 6-membered heterocycloalkylene; or L² is unsubstituted piperazino orunsubstituted piperidino; or L² is bicyclic fused heterocycloalkylene;or L² is an unsubstituted spirocyclic linker.

In some embodiments, E is a substituted or unsubstituted vinyl sulfonemoiety, substituted or unsubstituted vinyl sulfonamide moiety, or asubstituted or unsubstituted acrylamide moiety.

Further provided herein are pharmaceutical compositions comprising apharmaceutically acceptable excipient and a compound of the invention.

Also provided is a method of treating a disease in a patient in need ofsuch treatment, said method comprising administering a therapeuticallyeffective amount of a compound of any one of the compounds disclosedherein. In some embodiments, the disease is cancer, including but notlimited to colon cancer, colorectal cancer, pancreatic cancer, breastcancer, leukemia, or lung cancer (including non-small cell lung cancer).

Also provided are methods of modulating the activity of a Ras protein,including a H-Ras, N-Ras, or K-Ras protein, comprising contacting saidRas protein with an effective amount of a compound disclosed herein. Theactivity is, for example, GTPase activity, nucleotide exchange, effectorprotein binding, effector protein activation, guanine exchange factor(GEF) binding, GEF-facilitated nucleotide exchange, phosphate release,nucleotide release, nucleotide binding, Ras (e.g. K-Ras) subcellularlocalization, Ras (e.g. K-Ras) post-translational processing, or Ras(e.g. K-Ras) post-translational modifications. Said modulating can beincreasing the activity of said Ras (e.g. K-Ras) protein or reducing it.Said Ras (e.g. K-Ras) protein can be a human K-Ras protein. For example,a human K-Ras protein contains a G12C, G12D, G13C, or G13D mutation.

In some embodiments, a method of modulating a K-Ras protein is provided,said method comprising contacting said K-Ras protein with an effectiveamount of a compound described herein. Said modulating is, for example,modulation of K-Ras subcellular localization, K-Ras post-translationalprocessing, or a K-Ras post-translational modification. Said K-Rasprotein is, for example, a human K-Ras protein. In some embodiments,said human K-Ras protein contains a G12C, G12D, G13C, or G13D mutation.

In some embodiments, said Ras (e.g. K-Ras) protein is within abiological cell, for example a biological cell which forms part of anorganism.

Provided herein is also a Ras (e.g. K-Ras) protein covalently bound to acompound as disclosed herein, wherein said compound is covalently boundto a cysteine residue of said Ras (e.g. K-Ras) protein. Said covalentlymodified Ras protein may have a modulated activity relative to acontrol, wherein said activity is selected from GTPase activity,nucleotide exchange, effector protein binding, effector proteinactivation, guanine exchange factor (GEF) binding, GEF-facilitatednucleotide exchange, phosphate release, nucleotide release, nucleotidebinding, Ras subcellular localization, Ras post-translationalprocessing, and Ras post-translational modifications. In someembodiments, said Ras protein is a K-Ras protein which contains a G12Cmutation. The covalently bonded compound can be bonded to cysteineresidue 12. In other embodiments, the covalently modified Ras protein isa K-Ras protein which contains a G13C mutation. The covalently bondedcompound can be bonded to cysteine residue 13.

In other embodiments, a Ras (e.g. K-Ras) protein is provided which iscovalently bound to a compound disclosed herein, wherein said compoundis covalently bound to an aspartate residue of said Ras protein. Saidcovalently modified Ras protein may have a modulated activity relativeto a control, wherein said activity is selected from GTPase activity,nucleotide exchange, effector protein binding, effector proteinactivation, guanine exchange factor (GEF) binding, GEF-facilitatednucleotide exchange, phosphate release, nucleotide release, nucleotidebinding, Ras subcellular localization, Ras post-translationalprocessing, and Ras post-translational modifications. In someembodiments, said Ras protein is a K-Ras protein which contains a G12Dmutation. The covalently bonded compound can be bonded to aspartateresidue 12. In other embodiments, the covalently modified Ras protein isa K-Ras protein which contains a G13D mutation. The covalently bondedcompound can be bonded to aspartate residue 13.

Further provided herein is a method of identifying a covalent inhibitorof K-Ras protein comprising: contacting a K-Ras protein with a K-Rasinhibitor test compound; allowing said K-Ras inhibitor test compound tocovalently inhibit said K-Ras protein; and detecting the level ofcovalent inhibition of said K-Ras protein thereby identifying a covalentinhibitor of K-Ras protein. In some embodiments, the K-Ras inhibitortest compound is a Switch 2—Binding Pocket covalent inhibitor testcompound and said K-Ras protein is a G12C mutant K-Ras protein. Themethod may also comprise the steps of: contacting a wildtype K-Rasprotein with said Switch 2—Binding Pocket covalent inhibitor testcompound; allowing said Switch 2—Binding Pocket covalent inhibitor testcompound to inhibit said wildtype K-Ras protein; detecting the level ofinhibition of said wildtype K-Ras protein; comparing the level ofinhibition of said wildtype K-Ras protein to the level of covalentinhibition of said G12C mutant K-Ras protein, wherein a higher level ofcovalent inhibition of said G12C mutant K-Ras indicates said Switch2—Binding Pocket covalent inhibitor test compound is specific for saidG12C mutant K-Ras protein.

In some embodiments, said K-Ras inhibitor test compound is a Switch2—Binding Pocket covalent inhibitor test compound and said K-Ras proteinis a G12D mutant K-Ras protein. The method of identifying may alsocomprise the steps of: contacting a wildtype K-Ras protein with saidSwitch 2—Binding Pocket covalent inhibitor test compound; allowing saidSwitch 2—Binding Pocket covalent inhibitor test compound to inhibit saidwildtype K-Ras protein; detecting the level of inhibition of saidwildtype K-Ras protein; comparing the level of inhibition of saidwildtype K-Ras protein to the level of covalent inhibition of said G12Dmutant K-Ras protein, wherein a higher level of covalent inhibition ofsaid G12D mutant K-Ras indicates said Switch 2—Binding Pocket covalentinhibitor test compound is specific for said G12D mutant K-Ras protein.

In some embodiments, said K-Ras inhibitor test compound is a Switch2—Binding Pocket covalent inhibitor test compound and said K-Ras proteinis a G13C mutant K-Ras protein. The method of identifying may alsocomprise the steps of: contacting a wildtype K-Ras protein with saidSwitch 2—Binding Pocket covalent inhibitor test compound; allowing saidSwitch 2—Binding Pocket covalent inhibitor test compound to inhibit saidwildtype K-Ras protein; detecting the level of inhibition of saidwildtype K-Ras protein; comparing the level of inhibition of saidwildtype K-Ras protein to the level of covalent inhibition of said G13Cmutant K-Ras protein, wherein a higher level of covalent inhibition ofsaid G13C mutant K-Ras indicates said Switch 2—Binding Pocket covalentinhibitor test compound is specific for said G13C mutant K-Ras protein.

In some embodiments, said K-Ras inhibitor test compound is a Switch2—Binding Pocket covalent inhibitor test compound and said K-Ras proteinis a G13D mutant K-Ras protein. The method of identifying may alsocomprise the steps of: contacting a wildtype K-Ras protein with saidSwitch 2—Binding Pocket covalent inhibitor test compound; allowing saidSwitch 2—Binding Pocket covalent inhibitor test compound to inhibit saidwildtype K-Ras protein; detecting the level of inhibition of saidwildtype K-Ras protein; comparing the level of inhibition of saidwildtype K-Ras protein to the level of covalent inhibition of said G13Dmutant K-Ras protein, wherein a higher level of covalent inhibition ofsaid G13D mutant K-Ras indicates said Switch 2—Binding Pocket covalentinhibitor test compound is specific for said G13D mutant K-Ras protein.

Provided herein is a method of selectively modulating a Ras protein,said method comprising contacting said Ras protein with a compound whichcontacts at least one amino acid residue forming a Switch 2 bindingpocket of said Ras protein, wherein said at least one amino acid residueis selected from valine-7, valine-9, glycine-10, proline-34,threonine-58, glycine-60, glutamine-61, glutamate-62, glutamate-63,arginine-68, tyrosine-71, methionine-72, tyrosine-96, glutamine-99 andisoleucine-100 of said Ras protein, and wherein said compound covalentlyreacts with an amino acid residue of said Ras protein. In someembodiments, the compound binds to a K-Ras protein with a higher bindingaffinity as compared to a H-Ras protein. In some embodiments, saidcompound interacts with at least one of glycine-60, glutamate-62, orglutamate-63. In some embodiments, said interacting between said aminoacid residue and said compound involves hydrogen bonding, van der Waalsinteraction, ionic bonding, covalent bonding, or hydrophobicinteraction. In some embodiments, said compound fills space within saidSwitch 2 binding pocket. In some embodiments, said compound inhibitsK-Ras as measured by the fraction of protein covalently labeled by thecompound, wherein the compound is present in 50-fold excess and whereinthe fraction of protein covalently labeled is determined by massspectrometry. In some embodiments, said compound covalently reacts withan amino acid residue of said Ras (e.g. K-ras) protein. In someembodiments, said amino acid residue is cysteine-12 of K-Ras G12C mutantprotein.

Further provided is a method of designing a compound which covalentlybinds to a Switch 2 binding pocket of a K-Ras protein, the methodcomprising the steps of: (a) providing a structural model of a referencecompound bound to the Switch 2 binding pocket of the K-Ras protein,wherein the reference compound is non-covalently bound to said Switch 2binding pocket; (b) identifying a cysteine, aspartate, lysine, tyrosineor glutamate residue located in proximity to said Switch 2 bindingpocket when said reference compound is bound to said Switch 2 bindingpocket; (c) generating at least one additional structural model of atest compound bound to said Switch 2 binding pocket, wherein said testcompound comprises an electrophilic moiety; and (d) selecting said testcompound if said electrophilic moiety is located within bonding distanceof said cysteine residue when said test compound is bound to said Switch2 binding pocket.

Compounds are also provided having molecular dimensions compatible withthe shape of a K-Ras Switch 2 binding pocket wherein the compound, whenpresent in an aqueous solution comprising 200 μM of the compound and 4μM K-Ras, covalently binds to at least 50% of K-Ras proteins present insolution after 24 hours.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Ras cycles from inactive GDP-bound state to active GTP-boundstate. In the active conformation, Ras may interact with downstreameffector proteins. PI3K is unusual amongst effectors in that it makescritical contacts with the Switch 2 region of Ras. Structural datasuggest that other effectors, including Raf, only make direct contactswith the Switch 1 region.

FIG. 2: Structural insights into nucleotide binding by Ras. (A) Theconformation of Ras undergoes significant changes upon binding todifferent nucleotides. Especially affected are two regions of theprotein, termed switch 1 (residue 30-40, black) and Switch 2 (residue60-76, dark gray), that are involved in binding downstream effectors.Shown here are structures of wild-type Ras bound to GDP (PDB code: 4q21(Milburn M V, Tong L, deVos A M, Brünger A, Yamaizumi Z, Nishimura S,Kim S H. Science. 1990 Feb. 23; 247(4945):939-45), inactiveconformation) and GMPPCP (PDB code: 121p (Krengel, U., Thesis,Heidelberg, 1991), active conformation); sequence legend SEQ ID NO:1left, SEQ ID NO:2 right. (B) Detailed view of the nucleotide bindingpocket of the G12C mutant of Ras. This structure was solved in theShokat lab to 2.4 Å resolution. Labeled residues are either known toplay important roles in the biological function of Ras (oncogenicmutations often occur in G12, G13 and Q61) (Forbes, S. et al. Cosmic2005. Br J Cancer 94, 318-22 (2006)), can serve as potential sites forcysteine mutant for covalent attachment (C12, G13, S17, A18, Q30) orshow lysine residues that may serve as additional nucleophiles fordivalent probes (K16, K117, K147). The nucleophilic sulfur ofcysteine-12 is in close proximity to the terminal phosphate group ofGDP, supporting the idea of using this cysteine as nucleophilic anchorfor covalent (e.g. reversible, irreversible) modification; sequencelegend SEQ ID NO:3.

FIG. 3. Tethering to identify drug-like fragments that bind to K-RasG12C; Tethering depends on a complex equilibrium of disulfide exchangebetween compounds and reducing agent. K-RasG12C may exchange withcompounds binding in the nucleotide-binding pocket (square) orallosteric pocket (circle); mass spectrometry-based; reversible covalentinteraction based on complex equilibrium of disulfides; semi-highthroughput; identify low-affinity drug-like fragments to use asscaffolds; based on binding, not inhibition of activity.

FIG. 4. Compound (JO-01-189cbut) binding to Switch 2—Binding Pocket ofK-Ras. (A) Binding of JO-01-189cbut to the Switch 2—Binding Pocketinduces changes in the protein structure, including to the adjacentSwitch 2 region. For comparison wild-type Ras bound to GDP (PDB code:4q21², inactive conformation) and GMPPCP (PDB code: 121p³, activeconformation) are shown. Switch 1 (residue 30-40, black) and Switch 2(residue 60-76, dark gray) are colored for clarity; sequence legend SEQID NO:1 left, SEQ ID NO:2 right, SEQ ID NO:4 bottom. (B) JO-01-189cbutbinding to the Switch 2—Binding Pocket is shown in three-dimensionaldetail with interacting amino acids labeled; sequence legend SEQ IDNO:4.

FIG. 5. Two hits from screen of disulfide containing compounds.Percentages represent the amount of modified Ras in the presence of 100μM each of compound and BME. The screening hits all showed selectivityfor the mutant cysteine, causing minimal modification of wild-typeK-Ras. Addition of GDP had no significant effect on modification ofK-RasG12C by 6H05. Results from 2E07 show that it is possible to achievesome selectivity for K-RasG12C over H-RasG12C. These screens werecarried out using K-RasG12C truncated and K-Ras wild-type truncated.

FIG. 6. Structure and DR50 of 6H05 analogues. Compound JO-148A isslightly more potent than the related screening hit.

FIG. 7. Compound(ligand):protein contacts/interactions ofRasmed-055:G12C K-Ras, sequence legend (SEQ ID NO:4).

FIG. 8. Compound(ligand):protein contacts/interactions ofJO-01-189cbut:G12C K-Ras; sequence legend (SEQ ID NO:4).

FIGS. 9A-9B. Protein sequences for human H-Ras and K-Ras (includingsplice variants and mutants); in some embodiments, a Ras protein maycontain one or more amino acids at the amino terminus due to the designof expression constructs (e.g. GAMGS may be in embodiments of H-Ras G12Ctruncation or G in embodiments of K-Ras constructs), however, amino acidnumbering follows the physiological amino acid numbering not includingconstruct introduced amino terminus extra amino acids.

FIGS. 10A-10B. K-Ras*mant-d-GDP exchange with unlabeled GDP, half-life(single exponential) shown (stop-flow experiment with low magnesium).

FIGS. 11A-11B. K-Ras*mant-d-GDP exchange with unlabeled GDP or GTP,half-life (single exponential) shown (stop-flow experiment with lowmagnesium).

FIG. 12. Ras-079 shows same conformation in two different space groups(C2 vs. P212121); P212121 has switch 1 ordered in unseen conformation,metal present as well in K-Ras sequence legend (SEQ ID NO:4).

FIG. 13. Unusual metal coordination in new P212121 space group (Tyr-32)of K-Ras, sequence legend (SEQ ID NO:4).

FIGS. 14A-14B. Labeling of H-Ras G12C; labeling successful (>1 day,EDTA, 250 micM); only single labeling visible despite high conc.;Potential degradation products.

FIG. 15. Evidence of compound in H-Ras; 1 sigma 2fo-fc map shown,H-Ras*GDP*055, 1.18 A resolution, 0.1791 Rfree, sequence legend (SEQ IDNO:3).

FIG. 16. Compound is out of the pocket in H-Ras compared to K-Ras;H-Ras*GDP*055 (light gray), K-Ras*GDP*055 (dark gray); sequence legendlight gray (SEQ ID NO:3), dark gray (SEQ ID NO:4).

FIG. 17. Co-crystal structures show novel pocket, sequence legend (SEQID NO:4).

FIG. 18. Co-crystal structures show novel pocket; new polar interactionsin optimized compounds; inhibitors bind behind Switch II and disruptboth Switches; bind much more slowly to KrasGTP; switch conformationsare critical for activation downstream; may interfere with GTP binding;sequence legend (SEQ ID NO:4).

FIG. 19. G60A in Switch II is dominant negative, glycine-60 to alaninemutation is dominant negative; small changes in Switch II can have hugeconsequences for function; top Kras-G12C with Ras-055; bottom Kras-WTtruncated; sequence legend top (SEQ ID NO:4), bottom (SEQ ID NO: 16).

FIG. 20. Ras nucleotide exchange and protein interactions.

FIG. 21. Inhibitors block Ras activation—“OFF exchange”; similarinhibition seen in [a-32P]GTP “ON exchange”; working on plate-basedassay to test relative nucleotide affinities.

FIG. 22. Ras nucleotide exchange and protein interactions.

FIG. 23. Rafl-RBD pull-downs; inhibitors decrease Raf binding,especially in GTP-GDP mixtures; suggest inhibitors change relativeaffinity for nucleotides.

FIG. 24. H358 (G12C) cells less sensitive in high serum; 24 hr treatmentin 0.5% FBS followed by proliferation in 10% FBS; larger difference atlower cell density.

FIG. 25. Proliferation of human lung cancer cell lines; 24 hr treatmentin 0.5% FBS followed by proliferation in 10% FBS.

FIG. 26. Induction of pERK after treatment in G12C cells; in Brafmelanoma cells, Kras siRNA induces pERK.

FIGS. 27A-27B. Phosphosignaling after treatment with Ras-083.

FIG. 28. Proliferation of human lung cancer cell lines; 2,000cells/well; 24 hr treatment, 48 hr washout all in 10% FBS.

FIG. 29. Proliferation of human lung cancer cell lines; 24 hr treatment(0.5% FBS), 48 hr washout (10% FBS); now both G12C cell lines looksignificantly more sensitive to Ras-083.

FIG. 30. Proliferation of human lung cancer cell lines; 4,000cells/well; 24 hr treatment, 48 hr washout all at 10% FBS; 1 uMlapatinib.

FIG. 31. Raf1-RBD pull-downs; Ras-083 impairs binding of RasGTP toRaf1-RBD after EDTA-catalyzed exchange; Adding a mixture of GTP and GDPallows preferential binding to GDP even when GTP is in excess (10:1 and7:1); experiment performed as described herein.

FIG. 32. Compound binding to K-Ras alters affinities for GTP and GppNp(GNP), (competition experiments with mant-dGDP).

FIG. 33. IC50 of different nucleotides competing with mant-d-GDP (˜1micM); IC50 ratios (representative of relative affinities) shift greatlytowards GDP over GTP in case of the compound bound K-Ras.

FIGS. 34A-34B. Compound binding to K-Ras reduces SOS-mediated exchange(association of mant-d-GDP monitored).

FIGS. 35A-35B. Compound binding to K-Ras reduces SOS-mediated exchange(association of mant-d-GppNp monitored).

FIGS. 36A-36D. Compound binding to K-Ras reduces SOS-mediated exchange(dissociation of mant-d-GDP monitored).

FIG. 37. Labeling of K-Ras G12C loaded with GDP or GTP analog; fragmentsbind to GDP-loaded K-Ras G12C but not GTP-loaded K-Ras G12C; %modification with 100 μM fragment and 200 μM βME; figure legend SEQ IDNO:15.

FIG. 38. Concentration of fragment necessary for 50% modification ofK-RasG12C in presence of 100 μM βME, figure legend SEQ ID NO:15; severalrounds of inhibitor optimization lead to improved labeling at 200 μMβME. This series shows the effect of linker changes on labeling.

FIG. 39. 189Cbu selectively slows GEF-catalyzed nucleotide exchange byK-Ras G12C without affecting wild type K-Ras, figure legend SEQ ID NO:10 and SEQ ID NO: 11.

FIG. 40. Inhibitors induce formation of a pocket behind switch II;switch II is modeled from active (GMPPNP§) and inactive (GDP§)structures into the 189Cbu complex left; the model shows a steric clashbetween the inhibitor and residues from switch II in the activeconformation, suggesting these compounds may disrupt the active state ofRas and impair downstream signaling; left panel K-Ras G12C bound to189Cbu; § Model, switch II mapped onto 189Cu structure; figure legendSEQ ID NO:4.

FIG. 41. Ras cycles between an inactive GDP-bound state and an activeGTP-bound state; in the active conformation, Ras interacts withdownstream effector proteins such as Raf and PI3K; effectors interactwith Ras-GTP through switch I and switch II, which differ structurallybetween nucleotide states; oncogenic mutations in Ras (most frequentlyat positions 12, 13, or 61) disrupt GAP-facilitated GTP hydrolysis,kinetically locking Ras in the GTP-bound “on” state.

FIG. 42. Targeted glycine-12 to cysteine (G12C) mutant of K-Ras bytaking advantage of the high nucleophilicity of the mutant residue; mostcommon K-Ras mutation in lung cancer (˜9% NSCLC, COSMIC); adjacent tonucleotide site and switches; covalent handle enhances selectivity andpotency.

FIG. 43. Screened 480-compound library at 100 μM βME and 100 μMfragment; compounds modifying K-Ras G12C at >50% were considered hits;of 17 hit compounds, none caused >10% modification of wild type K-Ras,which contains a surface exposed cysteine (C118); two hits shown;fragments bind to GDP-loaded K-Ras but not GTP-loaded K-Ras; left panel% modification with 100 μM fragment and 100 μM βME; right panel %modification with 100 μM fragment and 200 μM βME.

DETAILED DESCRIPTION OF THE INVENTION Definitions

The abbreviations used herein have their conventional meaning within thechemical and biological arts. The chemical structures and formulae setforth herein are constructed according to the standard rules of chemicalvalency known in the chemical arts.

Where substituent groups are specified by their conventional chemicalformulae, written from left to right, they equally encompass thechemically identical substituents that would result from writing thestructure from right to left, e.g., —CH₂O— is equivalent to —OCH₂—.

The term “alkyl,” by itself or as part of another substituent, means,unless otherwise stated, a straight (i.e., unbranched) or branchedcarbon chain (or carbon), or combination thereof, which may be fullysaturated, mono- or polyunsaturated and can include mono-, di- andmultivalent radicals, having the number of carbon atoms designated(i.e., C₁-C₁₀ means one to ten carbons). Examples of saturatedhydrocarbon radicals include, but are not limited to, groups such asmethyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl,sec-butyl, (cyclohexyl)methyl, homologs and isomers of, for example,n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkylgroup is one having one or more double bonds or triple bonds Examples ofunsaturated alkyl groups include, but are not limited to, vinyl,2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl,3-(1,4-pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and thehigher homologs and isomers. An alkoxy is an alkyl attached to theremainder of the molecule via an oxygen linker (—O—).

The term “alkylene,” by itself or as part of another substituent, means,unless otherwise stated, a divalent radical derived from an alkyl, asexemplified, but not limited by, —CH₂CH₂CH₂CH₂—. Typically, an alkyl (oralkylene) group will have from 1 to 24 carbon atoms, with those groupshaving 10 or fewer carbon atoms being preferred in the presentinvention. A “lower alkyl” or “lower alkylene” is a shorter chain alkylor alkylene group, generally having eight or fewer carbon atoms. Theterm “alkenylene,” by itself or as part of another substituent, means,unless otherwise stated, a divalent radical derived from an alkene.

The term “heteroalkyl,” by itself or in combination with another term,means, unless otherwise stated, a stable straight or branched chain, orcombinations thereof, including at least one carbon atom and at leastone heteroatom selected from the group consisting of O, N, P, Si, and S,and wherein the nitrogen and sulfur atoms may optionally be oxidized,and the nitrogen heteroatom may optionally be quaternized. Theheteroatom(s) 0, N, P, S, B, As, and Si may be placed at any interiorposition of the heteroalkyl group or at the position at which the alkylgroup is attached to the remainder of the molecule. Examples include,but are not limited to: —CH₂—CH₂—O—CH₃, —CH₂—CH₂—NH—CH₃,—CH₂—CH₂—N(CH₃)—CH₃, —CH₂—S—CH₂—CH₃, —CH₂—CH₂, —S(O)—CH₃,—CH₂—CH₂—S(O)₂—CH₃, —CH═CH—O—CH₃, —Si(CH₃)₃, —CH₂—CH═N—OCH₃,—CH═CH—N(CH₃)—CH₃, —O—CH₃, —O—CH₂—CH₃, and —CN. Up to two or threeheteroatoms may be consecutive, such as, for example, —CH₂—NH—OCH₃ and—CH₂—O—Si(CH₃)₃.

Similarly, the term “heteroalkylene,” by itself or as part of anothersubstituent, means, unless otherwise stated, a divalent radical derivedfrom heteroalkyl, as exemplified, but not limited by,—CH₂—CH₂—S—CH₂—CH₂— and —CH₂—S—CH₂—CH₂—NH—CH₂—. For heteroalkylenegroups, heteroatoms can also occupy either or both of the chain termini(e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, andthe like). Still further, for alkylene and heteroalkylene linkinggroups, no orientation of the linking group is implied by the directionin which the formula of the linking group is written. For example, theformula —C(O)₂R′— represents both —C(O)₂R′— and —R′C(O)₂—. As describedabove, heteroalkyl groups, as used herein, include those groups that areattached to the remainder of the molecule through a heteroatom, such as—C(O)R′, —C(O)NR′, —NR′R″, —OR′, —SR′, and/or —SO₂R′. Where“heteroalkyl” is recited, followed by recitations of specificheteroalkyl groups, such as —NR′R″ or the like, it will be understoodthat the terms heteroalkyl and —NR′R″ are not redundant or mutuallyexclusive. Rather, the specific heteroalkyl groups are recited to addclarity. Thus, the term “heteroalkyl” should not be interpreted hereinas excluding specific heteroalkyl groups, such as —NR′R″ or the like.

The terms “cycloalkyl” and “heterocycloalkyl,” by themselves or incombination with other terms, mean, unless otherwise stated, cyclicversions of “alkyl” and “heteroalkyl,” respectively. Additionally, forheterocycloalkyl, a heteroatom can occupy the position at which theheterocycle is attached to the remainder of the molecule. Examples ofcycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl,and the like. Examples of heterocycloalkyl include, but are not limitedto, 1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl,3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl,tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl,1-piperazinyl, 2-piperazinyl, and the like. A “cycloalkylene” and a“heterocycloalkylene,” alone or as part of another substituent, means adivalent radical derived from a cycloalkyl and heterocycloalkyl,respectively.

The terms “halo” or “halogen,” by themselves or as part of anothersubstituent, mean, unless otherwise stated, a fluorine, chlorine,bromine, or iodine atom. Additionally, terms such as “haloalkyl” aremeant to include monohaloalkyl and polyhaloalkyl. For example, the term“halo(C₁-C₄)alkyl” includes, but is not limited to, fluoromethyl,difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl,3-bromopropyl, and the like.

The term “acyl” means, unless otherwise stated, —C(O)R where R is asubstituted or unsubstituted alkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl.

The term “aryl” means, unless otherwise stated, a polyunsaturated,aromatic, hydrocarbon substituent, which can be a single ring ormultiple rings (preferably from 1 to 3 rings) that are fused together(i.e., a fused ring aryl) or linked covalently. A fused ring aryl refersto multiple rings fused together wherein at least one of the fused ringsis an aryl ring. The term “heteroaryl” refers to aryl groups (or rings)that contain at least one heteroatom such as N, O, or S, wherein thenitrogen and sulfur atoms are optionally oxidized, and the nitrogenatom(s) are optionally quaternized. Thus, the term “heteroaryl” includesfused ring heteroaryl groups (i.e., multiple rings fused togetherwherein at least one of the fused rings is a heteroaromatic ring). A5,6-fused ring heteroarylene refers to two rings fused together, whereinone ring has 5 members and the other ring has 6 members, and wherein atleast one ring is a heteroaryl ring. Likewise, a 6,6-fused ringheteroarylene refers to two rings fused together, wherein one ring has 6members and the other ring has 6 members, and wherein at least one ringis a heteroaryl ring. And a 6,5-fused ring heteroarylene refers to tworings fused together, wherein one ring has 6 members and the other ringhas 5 members, and wherein at least one ring is a heteroaryl ring. Aheteroaryl group can be attached to the remainder of the moleculethrough a carbon or heteroatom. Non-limiting examples of aryl andheteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl,1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl,4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl,5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl,4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl,2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl,5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl,5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and6-quinolyl. Substituents for each of the above noted aryl and heteroarylring systems are selected from the group of acceptable substituentsdescribed below. An “arylene” and a “heteroarylene,” alone or as part ofanother substituent, mean a divalent radical derived from an aryl andheteroaryl, respectively. A heteroaryl group substituent may be a —O—bonded to a ring heteroatom nitrogen.

A fused ring heterocycloalkyl-aryl is an aryl fused to aheterocycloalkyl. A fused ring heterocycloalkyl-heteroaryl is aheteroaryl fused to a heterocycloalkyl. A fused ringheterocycloalkyl-cycloalkyl is a heterocycloalkyl fused to a cycloalkyl.A fused ring heterocycloalkyl-heterocycloalkyl is a heterocycloalkylfused to another heterocycloalkyl. Fused ring heterocycloalkyl-aryl,fused ring heterocycloalkyl-heteroaryl, fused ringheterocycloalkyl-cycloalkyl, or fused ringheterocycloalkyl-heterocycloalkyl may each independently beunsubstituted or substituted with one or more of the substitutentsdescribed herein. Spirocyclic rings are two or more rings whereinadjacent rings are attached through a single atom. The individual ringswithin spirocyclic rings may be identical or different. Individual ringsin spirocyclic rings may be substituted or unsubstituted and may havedifferent substituents from other individual rings within a set ofspirocyclic rings. Possible substituents for individual rings withinspirocyclic rings are the possible substituents for the same ring whennot part of spirocyclic rings (e.g. substitutents for cycloalkyl orheterocycloalkyl rings). Spirocyclic rings may be substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkylene,substituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heterocycloalkylene and individual rings within aspirocyclic ring group may be any of the immediately previous list,including having all rings of one type (e.g. all rings being substitutedheterocycloalkylene wherein each ring may be the same or differentsubstituted heterocycloalkylene). When referring to a spirocyclic ringsystem, heterocyclic spirocyclic rings means a spirocyclic rings whereinat least one ring is a heterocyclic ring and wherein each ring may be adifferent ring. When referring to a spirocyclic ring system, substitutedspirocyclic rings means that at least one ring is substituted and eachsubstituent may optionally be different.

The term “oxo,” as used herein, means an oxygen that is double bonded toa carbon atom.

The term “alkylsulfonyl,” as used herein, means a moiety having theformula —S(O₂)—R′, where R′ is a substituted or unsubstituted alkylgroup as defined above. R′ may have a specified number of carbons (e.g.,“C₁-C₄ alkylsulfonyl”).

Each of the above terms (e.g., “alkyl,” “heteroalkyl,” “aryl,” and“heteroaryl”) includes both substituted and unsubstituted forms of theindicated radical. Preferred substituents for each type of radical areprovided below.

Substituents for the alkyl and heteroalkyl radicals (including thosegroups often referred to as alkylene, alkenyl, heteroalkylene,heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, andheterocycloalkenyl) can be one or more of a variety of groups selectedfrom, but not limited to, —OR′, ═O, ═NR′, ═N—OR′, —NR′R″, —SR′,-halogen, —SiR′R″R′″, —OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″,—NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NR—C(NR′R″R′″)═NR″″,—NR—C(NR′R″)═NR′″, —S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NR′SO₂R′,—NR′NR″R′″, —ONR′R″, —NR′C═(O)NR″NR′″R″″, —CN, —NO₂, —NR′SO₂R″,—NR′C═(O)R″, —NR′C(O)—OR″, —NR′OR″, in a number ranging from zero to(2m′+1), where m′ is the total number of carbon atoms in such radical.R, R′, R″, R′″, and R″″ each preferably independently refer to hydrogen,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl (e.g., aryl substituted with 1-3 halogens),substituted or unsubstituted heteroaryl, substituted or unsubstitutedalkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups. When acompound of the invention includes more than one R group, for example,each of the R groups is independently selected as are each R′, R″, R′″,and R″″ group when more than one of these groups is present. When R′ andR″ are attached to the same nitrogen atom, they can be combined with thenitrogen atom to form a 4-, 5-, 6-, or 7-membered ring. For example,—NR′R″ includes, but is not limited to, 1-pyrrolidinyl and4-morpholinyl. From the above discussion of substituents, one of skillin the art will understand that the term “alkyl” is meant to includegroups including carbon atoms bound to groups other than hydrogengroups, such as haloalkyl (e.g., —CF₃ and —CH₂CF₃) and acyl (e.g.,—C(O)CH₃, —C(O)CF₃, —C(O)CH₂OCH₃, and the like).

Similar to the substituents described for the alkyl radical,substituents for the aryl and heteroaryl groups are varied and areselected from, for example: —OR′, —NR′R″, —SR′, -halogen, —SiR′R″R′″,—OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″, —NR″C(O)R′,—NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NR—C(NR′R″R′″)═NR″″, —NR—C(NR′R″)═NR′″,—S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NRSO₂R′, —NR′NR″R′″, —ONR′R″,—NR′C═(O)NR″NR′″R″″, —CN, —NO₂, —R′, —N₃, —CH(Ph)₂, fluoro(C₁-C₄)alkoxy,and fluoro(C₁-C₄)alkyl, —NR′SO₂R″, —NR′C═(O)R″, —NR′C(O)—OR″, —NR′OR″,in a number ranging from zero to the total number of open valences onthe aromatic ring system; and where R′, R″, R′″, and R″″ are preferablyindependently selected from hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, and substituted or unsubstitutedheteroaryl. When a compound of the invention includes more than one Rgroup, for example, each of the R groups is independently selected asare each R′, R″, R′″, and R″″ groups when more than one of these groupsis present.

Substituents for rings (e.g. cycloalkyl, heterocycloalkyl, aryl,heteroaryl, cycloalkylene, heterocycloalkylene, arylene, orheteroarylene) may be depicted as substituents on the ring rather thanon a specific atom of a ring (commonly referred to as a floatingsubstituent). In such a case, the substituent may be attached to any ofthe ring atoms (obeying the rules of chemical valency) and in the caseof fused rings or spirocyclic rings, a substituent depicted asassociated with one member of the fused rings or spirocyclic rings (afloating substituent on a single ring), may be a substituent on any ofthe fused rings or spirocyclic rings (a floating substituent on multiplerings). When a substituent is attached to a ring, but not a specificatom (a floating substituent), and a subscript for the substituent is aninteger greater than one, the multiple substituents may be on the sameatom, same ring, different atoms, different fused rings, differentspirocyclic rings, and each substituent may optionally be different.Where a point of attachment of a ring to the remainder of a molecule isnot limited to a single atom (a floating substituent), the attachmentpoint may be any atom of the ring and in the case of a fused ring orspirocyclic ring, any atom of any of the fused rings or spirocyclicrings while obeying the rules of chemical valency. Where a ring, fusedrings, or spirocyclic rings contain one or more ring heteroatoms and thering, fused rings, or spirocyclic rings are shown with one more morefloating substituents (including, but not limited to, points ofattachment to the remainder of the molecule), the floating substituentsmay be bonded to the heteroatoms. Where the ring heteroatoms are shownbound to one or more hydrogens (e.g. a ring nitrogen with two bonds toring atoms and a third bond to a hydrogen) in the structure or formulawith the floating substituent, when the heteroatom is bonded to thefloating substituent, the substituent will be understood to replace thehydrogen, while obeying the rules of chemical valency.

Two or more substituents may optionally be joined to form aryl,heteroaryl, cycloalkyl, or heterocycloalkyl groups. Such so-calledring-forming substituents are typically, though not necessarily, foundattached to a cyclic base structure. In one embodiment, the ring-formingsubstituents are attached to adjacent members of the base structure. Forexample, two ring-forming substituents attached to adjacent members of acyclic base structure create a fused ring structure. In anotherembodiment, the ring-forming substituents are attached to a singlemember of the base structure. For example, two ring-forming substituentsattached to a single member of a cyclic base structure create aspirocyclic structure. In yet another embodiment, the ring-formingsubstituents are attached to non-adjacent members of the base structure.

Two of the substituents on adjacent atoms of the aryl or heteroaryl ringmay optionally form a ring of the formula -T-C(O)—(CRR′)_(q)—U—, whereinT and U are independently —NR—, —O—, —CRR′—, or a single bond, and q isan integer of from 0 to 3. Alternatively, two of the substituents onadjacent atoms of the aryl or heteroaryl ring may optionally be replacedwith a substituent of the formula -A-(CH₂)_(r)—B—, wherein A and B areindependently —CRR′—, —O—, —NR—, —S—, —S(O)—, —S(O)₂—, —S(O)₂NR′—, or asingle bond, and r is an integer of from 1 to 4. One of the single bondsof the new ring so formed may optionally be replaced with a double bond.Alternatively, two of the substituents on adjacent atoms of the aryl orheteroaryl ring may optionally be replaced with a substituent of theformula —(CRR′)_(s)—X′— (C″R″R′″)_(d)—, where s and d are independentlyintegers of from 0 to 3, and X′ is —O—, —NR′—, —S—, —S(O)—, —S(O)₂—, or—S(O)₂NR′—. The substituents R, R′, R″, and R′″ are preferablyindependently selected from hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, and substituted or unsubstitutedheteroaryl.

As used herein, the terms “heteroatom” or “ring heteroatom” are meant toinclude, oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), Boron(B), Arsenic (As), and silicon (Si).

A “substituent group,” as used herein, means a group selected from thefollowing moieties: (A) oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, unsubstituted alkyl, unsubstituted heteroalkyl,unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstitutedaryl, unsubstituted heteroaryl, and (B) alkyl, heteroalkyl, cycloalkyl,heterocycloalkyl, aryl, and heteroaryl, substituted with at least onesubstituent selected from: (i) oxo, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, unsubstituted alkyl, unsubstituted heteroalkyl,unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstitutedaryl, unsubstituted heteroaryl, and (ii) alkyl, heteroalkyl, cycloalkyl,heterocycloalkyl, aryl, and heteroaryl, substituted with at least onesubstituent selected from: (a) oxo, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, unsubstituted alkyl, unsubstituted heteroalkyl,unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstitutedaryl, unsubstituted heteroaryl, and (b) alkyl, heteroalkyl, cycloalkyl,heterocycloalkyl, aryl, or heteroaryl, substituted with at least onesubstituent selected from: oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, unsubstituted alkyl, unsubstituted heteroalkyl,unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstitutedaryl, and unsubstituted heteroaryl.

A “size-limited substituent” or “size-limited substituent group,” asused herein, means a group selected from all of the substituentsdescribed above for a “substituent group,” wherein each substituted orunsubstituted alkyl is a substituted or unsubstituted C₁-C₂₀ alkyl, eachsubstituted or unsubstituted heteroalkyl is a substituted orunsubstituted 2 to 20 membered heteroalkyl, each substituted orunsubstituted cycloalkyl is a substituted or unsubstituted C₄-C₈cycloalkyl, and each substituted or unsubstituted heterocycloalkyl is asubstituted or unsubstituted 4 to 8 membered heterocycloalkyl.

A “lower substituent” or “lower substituent group,” as used herein,means a group selected from all of the substituents described above fora “substituent group,” wherein each substituted or unsubstituted alkylis a substituted or unsubstituted C₁-C₈ alkyl, each substituted orunsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8membered heteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₇ cycloalkyl, and each substituted orunsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7membered heterocycloalkyl.

In some embodiments, each substituted group described in the compoundsherein is substituted with at least one substituent group. Morespecifically, in some embodiments, each substituted alkyl, substitutedheteroalkyl, substituted cycloalkyl, substituted heterocycloalkyl,substituted aryl, substituted heteroaryl, substituted alkylene,substituted heteroalkylene, substituted cycloalkylene, substitutedheterocycloalkylene, substituted arylene, and/or substitutedheteroarylene described in the compounds herein are substituted with atleast one substituent group. In other embodiments, at least one or allof these groups are substituted with at least one size-limitedsubstituent group. In other embodiments, at least one or all of thesegroups are substituted with at least one lower substituent group.

In other embodiments of the compounds herein, each substituted orunsubstituted alkyl may be a substituted or unsubstituted C₁-C₂₀ alkyl,each substituted or unsubstituted heteroalkyl is a substituted orunsubstituted 2 to 20 membered heteroalkyl, each substituted orunsubstituted cycloalkyl is a substituted or unsubstituted C₃-C₈cycloalkyl, and/or each substituted or unsubstituted heterocycloalkyl isa substituted or unsubstituted 3 to 8 membered heterocycloalkyl. In someembodiments of the compounds herein, each substituted or unsubstitutedalkylene is a substituted or unsubstituted C₁-C₂₀ alkylene, eachsubstituted or unsubstituted heteroalkylene is a substituted orunsubstituted 2 to 20 membered heteroalkylene, each substituted orunsubstituted cycloalkylene is a substituted or unsubstituted C₃-C₈cycloalkylene, and/or each substituted or unsubstitutedheterocycloalkylene is a substituted or unsubstituted 3 to 8 memberedheterocycloalkylene.

In some embodiments, each substituted or unsubstituted alkyl is asubstituted or unsubstituted C₁-C₅ alkyl, each substituted orunsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8membered heteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₅-C₇ cycloalkyl, and/or each substitutedor unsubstituted heterocycloalkyl is a substituted or unsubstituted 5 to7 membered heterocycloalkyl. In some embodiments, each substituted orunsubstituted alkylene is a substituted or unsubstituted C₁-C₈ alkylene,each substituted or unsubstituted heteroalkylene is a substituted orunsubstituted 2 to 8 membered heteroalkylene, each substituted orunsubstituted cycloalkylene is a substituted or unsubstituted C₅-C₇cycloalkylene, and/or each substituted or unsubstitutedheterocycloalkylene is a substituted or unsubstituted 5 to 7 memberedheterocycloalkylene.

The term “pharmaceutically acceptable salts” is meant to include saltsof the active compounds that are prepared with relatively nontoxic acidsor bases, depending on the particular substituents found on thecompounds described herein. When compounds of the present inventioncontain relatively acidic functionalities, base addition salts can beobtained by contacting the neutral form of such compounds with asufficient amount of the desired base, either neat or in a suitableinert solvent. Examples of pharmaceutically acceptable base additionsalts include sodium, potassium, calcium, ammonium, organic amino, ormagnesium salt, or a similar salt. When compounds of the presentinvention contain relatively basic functionalities, acid addition saltscan be obtained by contacting the neutral form of such compounds with asufficient amount of the desired acid, either neat or in a suitableinert solvent. Examples of pharmaceutically acceptable acid additionsalts include those derived from inorganic acids like hydrochloric,hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric,monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,monohydrogensulfuric, hydriodic, or phosphorous acids and the like, aswell as the salts derived from relatively nontoxic organic acids likeacetic, propionic, isobutyric, maleic, malonic, benzoic, succinic,suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic,p-tolylsulfonic, citric, tartaric, oxalic, methanesulfonic, and thelike. Also included are salts of amino acids such as arginate and thelike, and salts of organic acids like glucuronic or galactunoric acidsand the like (see, for example, Berge et al., “Pharmaceutical Salts”,Journal of Pharmaceutical Science, 1977, 66, 1-19). Certain specificcompounds of the present invention contain both basic and acidicfunctionalities that allow the compounds to be converted into eitherbase or acid addition salts.

Thus, the compounds of the present invention may exist as salts, such aswith pharmaceutically acceptable acids. The present invention includessuch salts. Examples of such salts include hydrochlorides,hydrobromides, sulfates, methanesulfonates, nitrates, maleates,acetates, citrates, fumarates, tartrates (e.g., (+)-tartrates,(−)-tartrates, or mixtures thereof including racemic mixtures),succinates, benzoates, and salts with amino acids such as glutamic acid.These salts may be prepared by methods known to those skilled in theart.

The neutral forms of the compounds are preferably regenerated bycontacting the salt with a base or acid and isolating the parentcompound in the conventional manner. The parent form of the compounddiffers from the various salt forms in certain physical properties, suchas solubility in polar solvents.

In addition to salt forms, the present invention provides compounds,which are in a prodrug form. Prodrugs of the compounds described hereinare those compounds that readily undergo chemical changes underphysiological conditions to provide the compounds of the presentinvention. Additionally, prodrugs can be converted to the compounds ofthe present invention by chemical or biochemical methods in an ex vivoenvironment. For example, prodrugs can be slowly converted to thecompounds of the present invention when placed in a transdermal patchreservoir with a suitable enzyme or chemical reagent.

Certain compounds of the present invention can exist in unsolvated formsas well as solvated forms, including hydrated forms. In general, thesolvated forms are equivalent to unsolvated forms and are encompassedwithin the scope of the present invention. Certain compounds of thepresent invention may exist in multiple crystalline or amorphous forms.In general, all physical forms are equivalent for the uses contemplatedby the present invention and are intended to be within the scope of thepresent invention.

As used herein, the term “salt” refers to acid or base salts of thecompounds used in the methods of the present invention. Illustrativeexamples of acceptable salts are mineral acid (hydrochloric acid,hydrobromic acid, phosphoric acid, and the like) salts, organic acid(acetic acid, propionic acid, glutamic acid, citric acid and the like)salts, quaternary ammonium (methyl iodide, ethyl iodide, and the like)salts.

Certain compounds of the present invention possess asymmetric carbonatoms (optical or chiral centers) or double bonds; the enantiomers,racemates, diastereomers, tautomers, geometric isomers, stereoisomericforms that may be defined, in terms of absolute stereochemistry, as (R)-or (S)- or, as (D)- or (L)- for amino acids, and individual isomers areencompassed within the scope of the present invention. The compounds ofthe present invention do not include those which are known in art to betoo unstable to synthesize and/or isolate. The present invention ismeant to include compounds in racemic and optically pure forms.Optically active (R)- and (S)-, or (D)- and (L)-isomers may be preparedusing chiral synthons or chiral reagents, or resolved using conventionaltechniques. When the compounds described herein contain olefinic bondsor other centers of geometric asymmetry, and unless specified otherwise,it is intended that the compounds include both E and Z geometricisomers.

As used herein, the term “isomers” refers to compounds having the samenumber and kind of atoms, and hence the same molecular weight, butdiffering in respect to the structural arrangement or configuration ofthe atoms.

The term “tautomer,” as used herein, refers to one of two or morestructural isomers which exist in equilibrium and which are readilyconverted from one isomeric form to another.

It will be apparent to one skilled in the art that certain compounds ofthis invention may exist in tautomeric forms, all such tautomeric formsof the compounds being within the scope of the invention.

Unless otherwise stated, structures depicted herein are also meant toinclude all stereochemical forms of the structure; i.e., the R and Sconfigurations for each asymmetric center. Therefore, singlestereochemical isomers as well as enantiomeric and diastereomericmixtures of the present compounds are within the scope of the invention.

Unless otherwise stated, structures depicted herein are also meant toinclude compounds which differ only in the presence of one or moreisotopically enriched atoms. For example, compounds having the presentstructures except for the replacement of a hydrogen by a deuterium ortritium, or the replacement of a carbon by ¹³C- or ¹⁴C-enriched carbonare within the scope of this invention.

The compounds of the present invention may also contain unnaturalproportions of atomic isotopes at one or more of the atoms thatconstitute such compounds. For example, the compounds may beradiolabeled with radioactive isotopes, such as for example tritium(³H), iodine-125 (¹²⁵I), or carbon-14 (¹⁴C). All isotopic variations ofthe compounds of the present invention, whether radioactive or not, areencompassed within the scope of the present invention.

The symbol “—” denotes the point of attachment of a chemical moiety tothe remainder of a molecule or chemical formula.

It should be noted that throughout the application that alternatives arewritten in Markush groups, for example, each amino acid position thatcontains more than one possible amino acid. It is specificallycontemplated that each member of the Markush group should be consideredseparately, thereby comprising another embodiment, and the Markush groupis not to be read as a single unit.

A combinatorial chemical library is a collection of diverse chemicalcompounds generated by either chemical synthesis or biologicalsynthesis, by combining a number of chemical “building blocks” such asreagents. For example, a linear combinatorial chemical library such as apolypeptide library is formed by combining a set of chemical buildingblocks (amino acids) in every possible way for a given compound length(i.e., the number of amino acids in a polypeptide compound). Millions ofchemical compounds can be synthesized through such combinatorial mixingof chemical building blocks.

Preparation and screening of combinatorial chemical libraries is wellknown to those of skill in the art. Such combinatorial chemicallibraries include, but are not limited to, peptide libraries (see, e.g.,U.S. Pat. No. 5,010,175, Furka, Int. J Pept. Prot. Res. 37:487-493(1991) and Houghton et al., Nature 354:84-88 (1991)). Other chemistriesfor generating chemical diversity libraries can also be used. Suchchemistries include, but are not limited to: peptoids (e.g., PCTPublication No. WO 91/19735), encoded peptides (e.g., PCT Publication WO93/20242), random bio-oligomers (e.g., PCT Publication No. WO 92/00091),benzodiazepines (e.g., U.S. Pat. No. 5,288,514), diversomers such ashydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat.Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides (Hagiharaet al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidalpeptidomimetics with glucose scaffolding (Hirschmann et al., J. Amer.Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of smallcompound libraries (Chen et al., J. Amer. Chem. Soc. 116:2661 (1994)),oligocarbamates (Cho et al., Science 261:1303 (1993)), and/or peptidylphosphonates (Campbell et al., J. Org. Chem. 59:658 (1994)), nucleicacid libraries (see Ausubel, Berger and Sambrook, all supra), peptidenucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), antibodylibraries (see, e.g., Vaughn et al., Nature Biotechnology, 14(3):309-314(1996) and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang etal., Science, 274:1520-1522 (1996) and U.S. Pat. No. 5,593,853). Themethods above may be used to synthesize single molecular species.

The terms “a” or “an,” as used in herein means one or more. In addition,the phrase “substituted with a[n],” as used herein, means the specifiedgroup may be substituted with one or more of any or all of the namedsubstituents. For example, where a group, such as an alkyl or heteroarylgroup, is “substituted with an unsubstituted C₁-C₂₀ alkyl, orunsubstituted 2 to 20 membered heteroalkyl,” the group may contain oneor more unsubstituted C₁-C₂₀ alkyls, and/or one or more unsubstituted 2to 20 membered heteroalkyls. Moreover, where a moiety is substitutedwith an R substituent, the group may be referred to as “R-substituted.”Where a moiety is R-substituted, the moiety is substituted with at leastone R substituent and each R substituent is optionally different.

Description of compounds of the present invention is limited byprinciples of chemical bonding known to those skilled in the art.Accordingly, where a group may be substituted by one or more of a numberof substituents, such substitutions are selected so as to comply withprinciples of chemical bonding and to give compounds which are notinherently unstable and/or would be known to one of ordinary skill inthe art as likely to be unstable under ambient conditions, such asaqueous, neutral, and several known physiological conditions. Forexample, a heterocycloalkyl or heteroaryl is attached to the remainderof the molecule via a ring heteroatom in compliance with principles ofchemical bonding known to those skilled in the art thereby avoidinginherently unstable compounds.

The terms “treating” or “treatment” refers to any indicia of success inthe treatment or amelioration of an injury, disease, pathology orcondition, including any objective or subjective parameter such asabatement; remission; diminishing of symptoms or making the injury,pathology or condition more tolerable to the patient; slowing in therate of degeneration or decline; making the final point of degenerationless debilitating; improving a patient's physical or mental well-being.The treatment or amelioration of symptoms can be based on objective orsubjective parameters; including the results of a physical examination,neuropsychiatric exams, and/or a psychiatric evaluation. For example,the certain methods presented herein successfully treat cancer bydecreasing the incidence of cancer and or causing remission of cancer.In some embodiments of the compositions or methods described herein,treating cancer includes slowing the rate of growth or spread of cancercells, reducing metastasis, or reducing the growth of metastatic tumors.The term “treating” and conjugations thereof, include prevention of aninjury, pathology, condition, or disease.

An “effective amount” is an amount sufficient for a compound toaccomplish a stated purpose relative to the absence of the compound(e.g. achieve the effect for which it is administered, treat a disease,reduce enzyme activity, increase enzyme activity, reduce signalingpathway, reduce one or more symptoms of a disease or condition (e.g.reduce GTPase activity in a cell, increase GTPase activity, reducesignaling pathway stimulated by GTP bound Ras (e.g. K-Ras), reduce thesignaling pathway activity of Ras, reduce the signaling pathway activityof K-Ras, reduce the signaling pathway activity of K-Ras4A, reduce thesignaling pathway activity of K-Ras4B, reduce the signaling pathwayactivity of H-Ras, reduce the signaling pathway activity of N-Ras,reduce the signaling pathway activity of K-Ras G12C, reduce thesignaling pathway activity of K-Ras G13C, reduce the signaling pathwayactivity of K-Ras G13D, reduce the signaling pathway activity of K-RasG12D, reduce the signaling pathway activity of a mutant K-Ras, increasethe activity of Ras, increase the activity of K-Ras, increase theactivity of K-Ras4A, increase the activity of K-Ras4B, increase theactivity of H-Ras, increase the activity of N-Ras, increase the activityof K-Ras G12C, increase the activity of K-Ras G13C, increase theactivity of K-Ras G12D, increase the activity of K-Ras G13D, increasethe activity of a mutant K-Ras, inhibit the binding of K-Ras to SOS,inhibit the binding of K-Ras to a GEF, inhibit nucleotide exchange). Anexample of an “effective amount” is an amount sufficient to contributeto the treatment, prevention, or reduction of a symptom or symptoms of adisease, which could also be referred to as a “therapeutically effectiveamount.” A “reduction” of a symptom or symptoms (and grammaticalequivalents of this phrase) means decreasing of the severity orfrequency of the symptom(s), or elimination of the symptom(s). A“prophylactically effective amount” of a drug is an amount of a drugthat, when administered to a subject, will have the intendedprophylactic effect, e.g., preventing or delaying the onset (orreoccurrence) of an injury, disease, pathology or condition, or reducingthe likelihood of the onset (or reoccurrence) of an injury, disease,pathology, or condition, or their symptoms. The full prophylactic effectdoes not necessarily occur by administration of one dose, and may occuronly after administration of a series of doses. Thus, a prophylacticallyeffective amount may be administered in one or more administrations. An“activity decreasing amount,” as used herein, refers to an amount ofantagonist required to decrease the activity of an enzyme relative tothe absence of the antagonist. A “function disrupting amount,” as usedherein, refers to the amount of antagonist required to disrupt thefunction of an enzyme or protein relative to the absence of theantagonist (e.g. disrupt the protein-protein interaction between K-Rasand a signaling pathway binding protein such as PI3K, disrupt theinteraction of K-Ras and GEF, disrupt the interaction of K-Ras and SOS,disrupt the interaction of K-Ras with Raf). The exact amounts willdepend on the purpose of the treatment, and will be ascertainable by oneskilled in the art using known techniques (see, e.g., Lieberman,Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Scienceand Technology of Pharmaceutical Compounding (1999); Pickar, DosageCalculations (1999); and Remington: The Science and Practice ofPharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott, Williams &Wilkins).

“Control” or “control experiment” is used in accordance with its plainordinary meaning and refers to an experiment in which the subjects orreagents of the experiment are treated as in a parallel experimentexcept for omission of a procedure, reagent, or variable of theexperiment. In some instances, the control is used as a standard ofcomparison in evaluating experimental effects. In some embodiments, acontrol is the measurement of the activity (e.g. GTPase activity,protein-protein interaction, signaling pathway) of a protein (e.g. Ras,K-Ras, mutant K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G13C, K-Ras G13D) inthe absence of a compound as described herein (including embodiments,examples, Table 1, 2, 3, 4, or 5).

“Contacting” is used in accordance with its plain ordinary meaning andrefers to the process of allowing at least two distinct species (e.g.chemical compounds including biomolecules, or cells) to becomesufficiently proximal to react, interact or physically touch. It shouldbe appreciated; however, the resulting reaction product can be produceddirectly from a reaction between the added reagents or from anintermediate from one or more of the added reagents which can beproduced in the reaction mixture.

The term “contacting” may include allowing two species to react,interact, or physically touch, wherein the two species may be a compoundas described herein and a protein or enzyme (e.g. Ras, K-Ras, H-Ras,N-Ras, K-Ras4A, K-Ras4B, mutant Ras, mutant K-Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D). In some embodiments, the protein may beK-Ras. In some embodiments, the protein may be a mutant K-Ras (e.g.K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D). In some embodiments,the protein may be K-Ras4A. In some embodiments, the protein may beK-Ras4B. In some embodiments contacting includes allowing a compounddescribed herein to interact with a protein or enzyme that is involvedin a signaling pathway. In some embodiments contacting includes allowinga compound described herein to interact with a Switch 2—Binding Pocket.

As defined herein, the term “inhibition”, “inhibit”, “inhibiting” andthe like in reference to a protein-inhibitor interaction meansnegatively affecting (e.g. decreasing) the activity or function of theprotein (e.g. decreasing the signaling pathway stimulated by GTP boundRas (e.g. K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D),nucleotide exchange, effector protein binding, effector proteinactivation, guanine exchange factor (GEF) binding, SOS binding,GEF-facilitated nucleotide exchange, phosphate release, nucleotiderelease, nucleotide binding) relative to the activity or function of theprotein in the absence of the inhibitor (e.g. mutant K-Ras inhibitor,activated K-Ras inhibitor). In some embodiments inhibition refers toreduction of a disease or symptoms of disease. In some embodiments,inhibition refers to a reduction in the activity of a signaltransduction pathway or signaling pathway (e.g. reduction of a pathwayinvolving GTP bound Ras (e.g. K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D), reduction of a pathway involving mutant K-Ras (e.g. K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)). Thus, inhibition includes,at least in part, partially or totally blocking stimulation, decreasing,preventing, or delaying activation, or inactivating, desensitizing, ordown-regulating the signaling pathway or enzymatic activity or theamount of a protein (e.g. K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D). In some embodiments, inhibition refers to inhibition ofinteractions of Ras (K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) with signaling pathway binding partners (e.g. PI3K, SOS, Raf). Insome embodiments, inhibition refers to inhibition of interactions of Raswith a GEF (e.g. SOS).

The term “modulator” refers to a composition that increases or decreasesthe level of a target molecule or the function (e.g. GTPase activity,nucleotide exchange, effector protein binding, effector proteinactivation, guanine exchange factor (GEF) binding, SOS binding,GEF-facilitated nucleotide exchange, phosphate release, nucleotiderelease, nucleotide binding) of a target molecule or the physical state(e.g. Ras subcellular localization, Ras post-translational processing,Ras post-translational modifications) of the target of the molecule(e.g. a target may be K-Ras and the function may be to hydrolyze GTP oractivate a signaling pathway that is activated by GTP bound K-Ras,interaction of K-Ras with protein binding partners (e.g. PI3K, SOS,Raf)). In some embodiments, a GTPase modulator is a compound thatreduces the activity of a GTPase in a cell. In some embodiments, aGTPase modulator is a compound that increases the activity of a GTPasein a cell. In some embodiments, a GTPase modulator is a compound thatreduces the signaling pathway in a cell that is activated by the GTPbound form of Ras. In some embodiments, a GTPase modulator is a compoundthat increases the signaling pathway in a cell that is activated by theGTP bound form of Ras. In some embodiments, a K-Ras disease modulator isa compound that reduces the severity of one or more symptoms of adisease associated with K-Ras (e.g. cancer, metastatic cancer). A K-Rasmodulator is a compound that increases or decreases the activity orfunction or level of activity or level of function of K-Ras or level ofK-Ras or level of K-Ras in a particular physical state. A mutant K-Rasmodulator is a compound that that increases or decreases the activity orfunction or level of activity or level of function of mutant K-Ras orlevel of mutant K-Ras or level of mutant K-Ras in a particular physicalstate. A K-Ras G12C modulator, K-Ras G12D modulator, K-Ras G13Cmodulator, or K-Ras G13D modulator is a compound that increases ordecreases the activity or function or level of activity or level offunction of that particular mutant K-Ras or level of that particularmutant K-Ras or level of that particular mutant K-Ras in a particularphysical state. A K-Ras inhibitor is a compound that decreases theactivity or function or level of activity or level of function of K-Rasor level of K-Ras or level of K-Ras in a particular physical state. Amutant K-Ras inhibitor is a compound that that decreases the activity orfunction or level of activity or level of function of mutant K-Ras orlevel of mutant K-Ras or level of mutant K-Ras in a particular physicalstate. A K-Ras G12C inhibitor, K-Ras G12D inhibitor, K-Ras G13Cinhibitor, or K-Ras G13D inhibitor is a compound that decreases theactivity or function or level of activity or level of function of thatparticular mutant K-Ras or level of that particular mutant K-Ras orlevel of that particular mutant K-Ras in a particular physical state.

The term “modulate” is used in accordance with its plain ordinarymeaning and refers to the act of changing or varying one or moreproperties. “Modulation” refers to the process of changing or varyingone or more properties. For example, as applied to the effects of amodulator on a target protein, to modulate means to change by increasingor decreasing a property or function of the target molecule or theamount of the target molecule.

“Patient” or “subject in need thereof” refers to a living organismsuffering from or prone to a disease or condition that can be treated byadministration of a pharmaceutical composition as provided herein.Non-limiting examples include humans, other mammals, bovines, rats,mice, dogs, monkeys, goat, sheep, cows, deer, and other non-mammaliananimals. In some embodiments, a patient is human.

“Disease” or “condition” refer to a state of being or health status of apatient or subject capable of being treated with the compounds ormethods provided herein. In some embodiments, the disease is a diseaserelated to (e.g. caused by) a mutant Ras. In some embodiments, thedisease is a disease related to (e.g. caused by) a mutant K-Ras (e.g.K-Ras G12C, G13C, G12D, or G13D) or aberrant K-Ras signaling pathwayactivity (e.g. lung cancer, breast cancer, colon cancer, colorectalcancer, pancreatic cancer, leukemia). Examples of diseases, disorders,or conditions include, but are not limited to cancer. Examples ofdiseases, disorders, or conditions include, but are not limited toMYH-associated polyposis. In some instances, “disease” or “condition”refers to cancer. In some instances, “disease” or “condition” refers toMYH-associated polyposis. In some further instances, “cancer” refers tohuman cancers and carcinomas, sarcomas, adenocarcinomas, lymphomas,leukemias, etc., including solid and lymphoid cancers, kidney, breast,lung, bladder, colon, ovarian, prostate, pancreas, stomach, brain, headand neck, skin, uterine, testicular, glioma, esophagus, and livercancer, including hepatocarcinoma, lymphoma, including B-acutelymphoblastic lymphoma, non-Hodgkin's lymphomas (e.g., Burkitt's, SmallCell, and Large Cell lymphomas), Hodgkin's lymphoma, leukemia (includingAML, ALL, and CML), or multiple myeloma.

As used herein, the term “cancer” refers to all types of cancer,neoplasm or malignant tumors found in mammals (e.g. humans), includingleukemia, carcinomas and sarcomas. Exemplary cancers that may be treatedwith a compound or method provided herein include cancer of the thyroid,endocrine system, brain, breast, cervix, colon, head & neck, liver,kidney, lung, non-small cell lung, melanoma, mesothelioma, ovary,sarcoma, stomach, uterus, Medulloblastoma, colorectal cancer, pancreaticcancer. Additional examples include, Hodgkin's Disease, Non-Hodgkin'sLymphoma, multiple myeloma, neuroblastoma, glioma, glioblastomamultiforme, ovarian cancer, rhabdomyosarcoma, primary thrombocytosis,primary macroglobulinemia, primary brain tumors, cancer, malignantpancreatic insulanoma, malignant carcinoid, urinary bladder cancer,premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer,neuroblastoma, esophageal cancer, genitourinary tract cancer, malignanthypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms ofthe endocrine or exocrine pancreas, medullary thyroid cancer, medullarythyroid carcinoma, melanoma, colorectal cancer, papillary thyroidcancer, hepatocellular carcinoma, or prostate cancer.

The term “leukemia” refers broadly to progressive, malignant diseases ofthe blood-forming organs and is generally characterized by a distortedproliferation and development of leukocytes and their precursors in theblood and bone marrow. Leukemia is generally clinically classified onthe basis of (1) the duration and character of the disease-acute orchronic; (2) the type of cell involved; myeloid (myelogenous), lymphoid(lymphogenous), or monocytic; and (3) the increase or non-increase inthe number abnormal cells in the blood-leukemic or aleukemic(subleukemic). Exemplary leukemias that may be treated with a compoundor method provided herein include, for example, acute nonlymphocyticleukemia, chronic lymphocytic leukemia, acute granulocytic leukemia,chronic granulocytic leukemia, acute promyelocytic leukemia, adultT-cell leukemia, aleukemic leukemia, a leukocythemic leukemia,basophylic leukemia, blast cell leukemia, bovine leukemia, chronicmyelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilicleukemia, Gross' leukemia, hairy-cell leukemia, hemoblastic leukemia,hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia,acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia,lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia,lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia,megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia,myeloblastic leukemia, myelocytic leukemia, myeloid granulocyticleukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cellleukemia, multiple myeloma, plasmacytic leukemia, promyelocyticleukemia, Rieder cell leukemia, Schilling's leukemia, stem cellleukemia, subleukemic leukemia, or undifferentiated cell leukemia.

The term “sarcoma” generally refers to a tumor which is made up of asubstance like the embryonic connective tissue and is generally composedof closely packed cells embedded in a fibrillar or homogeneoussubstance. Sarcomas that may be treated with a compound or methodprovided herein include a chondrosarcoma, fibrosarcoma, lymphosarcoma,melanosarcoma, myxosarcoma, osteosarcoma, Abemethy's sarcoma, adiposesarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma,botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma,Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing'ssarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma,granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmentedhemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma,immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma,Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymomasarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma,serocystic sarcoma, synovial sarcoma, or telangiectaltic sarcoma.

The term “melanoma” is taken to mean a tumor arising from themelanocytic system of the skin and other organs. Melanomas that may betreated with a compound or method provided herein include, for example,acral-lentiginous melanoma, amelanotic melanoma, benign juvenilemelanoma, Cloudman's melanoma, S91 melanoma, Harding-Passey melanoma,juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodularmelanoma, subungal melanoma, or superficial spreading melanoma.

The term “carcinoma” refers to a malignant new growth made up ofepithelial cells tending to infiltrate the surrounding tissues and giverise to metastases. Exemplary carcinomas that may be treated with acompound or method provided herein include, for example, medullarythyroid carcinoma, familial medullary thyroid carcinoma, acinarcarcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cysticcarcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolarcarcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinomabasocellulare, basaloid carcinoma, basosquamous cell carcinoma,bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogeniccarcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorioniccarcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma,cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum,cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma,carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiermoidcarcinoma, carcinoma epitheliale adenoides, exophytic carcinoma,carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma,gelatinous carcinoma, giant cell carcinoma, carcinoma gigantocellulare,glandular carcinoma, granulosa cell carcinoma, hair-matrix carcinoma,hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma,hyaline carcinoma, hypernephroid carcinoma, infantile embryonalcarcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelialcarcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large-cellcarcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatouscarcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullarycarcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma,carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma,carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes,nasopharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans,osteoid carcinoma, papillary carcinoma, periportal carcinoma,preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma,renal cell carcinoma of kidney, reserve cell carcinoma, carcinomasarcomatodes, schneiderian carcinoma, scirrhous carcinoma, carcinomascroti, signet-ring cell carcinoma, carcinoma simplex, small-cellcarcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cellcarcinoma, carcinoma spongiosum, squamous carcinoma, squamous cellcarcinoma, string carcinoma, carcinoma telangiectaticum, carcinomatelangiectodes, transitional cell carcinoma, carcinoma tuberosum,tuberous carcinoma, verrucous carcinoma, or carcinoma villosum.

“Ras associated cancer” (also referred to herein as “Ras relatedcancer”) refers to a cancer caused by aberrant Ras activity orsignaling. A “cancer associated with aberrant K-Ras activity” (alsoreferred to herein as “K-Ras related cancer”) is a cancer caused byaberrant K-Ras activity or signaling (e.g. a mutant K-Ras). K-Rasrelated cancers may include lung cancer, non-small cell lung cancer,breast cancer, leukemia, pancreatic cancer, colon cancer, colorectalcancer. Other cancers that are associated with aberrant activity of oneor more of Ras, K-Ras, H-Ras, N-Ras, mutant K-Ras (including K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D mutants), mutant N-Ras, and mutantH-Ras are well known in the art and determining such cancers are withinthe skill of a person of skill in the art.

“Pharmaceutically acceptable excipient” and “pharmaceutically acceptablecarrier” refer to a substance that aids the administration of an activeagent to and absorption by a subject and can be included in thecompositions of the present invention without causing a significantadverse toxicological effect on the patient. Non-limiting examples ofpharmaceutically acceptable excipients include water, NaCl, normalsaline solutions, lactated Ringer's, normal sucrose, normal glucose,binders, fillers, disintegrants, lubricants, coatings, sweeteners,flavors, salt solutions (such as Ringer's solution), alcohols, oils,gelatins, carbohydrates such as lactose, amylose or starch, fatty acidesters, hydroxymethycellulose, polyvinyl pyrrolidine, and colors, andthe like. Such preparations can be sterilized and, if desired, mixedwith auxiliary agents such as lubricants, preservatives, stabilizers,wetting agents, emulsifiers, salts for influencing osmotic pressure,buffers, coloring, and/or aromatic substances and the like that do notdeleteriously react with the compounds of the invention. One of skill inthe art will recognize that other pharmaceutical excipients are usefulin the present invention.

The term “preparation” is intended to include the formulation of theactive compound with encapsulating material as a carrier providing acapsule in which the active component with or without other carriers, issurrounded by a carrier, which is thus in association with it.Similarly, cachets and lozenges are included. Tablets, powders,capsules, pills, cachets, and lozenges can be used as solid dosage formssuitable for oral administration.

As used herein, the term “administering” means oral administration,administration as a suppository, topical contact, intravenous,intraperitoneal, intramuscular, intralesional, intrathecal, intranasalor subcutaneous administration, or the implantation of a slow-releasedevice, e.g., a mini-osmotic pump, to a subject. Administration is byany route, including parenteral and transmucosal (e.g., buccal,sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal).Parenteral administration includes, e.g., intravenous, intramuscular,intra-arteriole, intradermal, subcutaneous, intraperitoneal,intraventricular, and intracranial. Other modes of delivery include, butare not limited to, the use of liposomal formulations, intravenousinfusion, transdermal patches, etc. By “co-administer” it is meant thata composition described herein is administered at the same time, justprior to, or just after the administration of one or more additionaltherapies, for example cancer therapies such as chemotherapy, hormonaltherapy, radiotherapy, or immunotherapy. The compounds of the inventioncan be administered alone or can be coadministered to the patient.Coadministration is meant to include simultaneous or sequentialadministration of the compounds individually or in combination (morethan one compound). Thus, the preparations can also be combined, whendesired, with other active substances (e.g. to reduce metabolicdegradation). The compositions of the present invention can be deliveredby transdermally, by a topical route, formulated as applicator sticks,solutions, suspensions, emulsions, gels, creams, ointments, pastes,jellies, paints, powders, and aerosols.

The term “administer (or administering) a Ras inhibitor” meansadministering a compound that inhibits the activity or level (e.g.amount) or level of a signaling pathway of one or more Ras proteins(e.g. a Ras inhibitor, K-Ras inhibitor, N-Ras inhibitor, H-Rasinhibitor, mutant K-Ras inhibitor, K-Ras G12C inhibitor, K-Ras G13Cinhibitor, K-Ras G12D inhibitor, K-Ras G13D inhibitor) to a subject.Administration may include, without being limited by mechanism, allowingsufficient time for the Ras inhibitor to reduce the activity of one ormore Ras proteins or for the Ras inhibitor to reduce one or moresymptoms of a disease (e.g. cancer, wherein the Ras inhibitor may arrestthe cell cycle, slow the cell cycle, reduce DNA replication, reduce cellreplication, reduce cell growth, reduce metastasis, or cause celldeath). The term “administer (or administering) a K-Ras inhibitor” meansadministering a compound that inhibits the activity or level (e.g.amount) or level of a signaling pathway of one or more K-Ras proteins(K-Ras, mutant K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G13C, K-Ras G13D).

The term “associated” or “associated with” in the context of a substanceor substance activity or function associated with a disease (e.g. aprotein associated disease, a cancer associated with aberrant Rasactivity, K-Ras associated cancer, mutant K-Ras associated cancer,activated K-Ras associated cancer, K-Ras G12C associated cancer, K-RasG13C associated cancer, K-Ras G12D associated cancer, K-Ras G13Dassociated cancer) means that the disease (e.g. cancer) is caused by (inwhole or in part), or a symptom of the disease is caused by (in whole orinpart) the substance or substance activity or function. For example, acancer associated with aberrant Ras activity or function may be a cancerthat results (entirely or partially) from aberrant Ras activity orfunction (e.g. enzyme activity, protein-protein interaction, signalingpathway) or a cancer wherein a particular symptom of the disease iscaused (entirely or partially) by aberrant Ras activity or function. Asused herein, what is described as being associated with a disease, if acausative agent, could be a target for treatment of the disease. Forexample, a cancer associated with aberrant Ras activity or function or aRas associated cancer, may be treated with a Ras modulator or Rasinhibitor, in the instance where increased Ras activity or function(e.g. signaling pathway activity) causes the cancer. For example, acancer associated with K-Ras G12C may be a cancer that a subject withK-Ras G12C is at higher risk of developing as compared to a subjectwithout K-Ras G12C.

The term “aberrant” as used herein refers to different from normal. Whenused to describe enzymatic activity, aberrant refers to activity that isgreater or less than a normal control or the average of normalnon-diseased control samples. Aberrant activity may refer to an amountof activity that results in a disease, wherein returning the aberrantactivity to a normal or non-disease-associated amount (e.g. byadministering a compound or using a method as described herein), resultsin reduction of the disease or one or more disease symptoms.

The term “electrophilic chemical moiety” is used in accordance with itsplain ordinary chemical meaning and refers to a monovalent chemicalgroup that is electrophilic.

The term “Ras” refers to one or more of the family of human Ras GTPaseproteins (e.g. K-Ras, H-Ras, N-Ras). The term “K-Ras” refers to thenucleotide sequences or proteins of human K-Ras (e.g. human K-Ras4A(NP_203524.1), human K-Ras4B (NP_004976.2), or both K-Ras4A andK-Ras4B). The term “K-Ras” includes both the wild-type form of thenucleotide sequences or proteins as well as any mutants thereof. In someembodiments, “K-Ras” is wild-type K-Ras. In some embodiments, “K-Ras” isone or more mutant forms. The term “K-Ras” XYZ refers to a nucleotidesequence or protein of a mutant K-Ras wherein the Y numbered amino acidof K-Ras that has an X amino acid in the wildtype instead has a Z aminoacid in the mutant (e.g. K-Ras G12C has a G in wildtype protein but a Cin the K-Ras G12C mutant protein). In some embodiments K-Ras refers toK-Ras4A and K-Ras4B. In some embodiments, K-Ras refers to K-Ras4A. Insome embodiments, K-Ras refers to K-Ras4B.

The term “Ras inhibitor test compound” as used herein refers to acompound that is being characterized in an assay for the ability toinhibit an activity, function, or level (e.g. amount) of a Ras protein.The term “K-Ras inhibitor test compound” as used herein refers to acompound that is being characterized in an assay for the ability toinhibit an activity, function, or level (e.g. amount) of K-Ras protein.A “Switch 2—Binding Pocket covalent inhibitor test compound” is a Rasinhibitor test compound that binds to a Ras Switch 2—Binding Pocket andis being tested for the ability to covalently inhibit an activity,function, or level (e.g. amount) of a Ras protein.

The term “signaling pathway” as used herein refers to a series ofinteractions between cellular and optionally extra-cellular components(e.g. proteins, nucleic acids, small molecules, ions, lipids) thatconveys a change in one component to one or more other components, whichin turn may convey a change to additional components, which isoptionally propogated to other signaling pathway components. Forexample, binding of a K-Ras with a compound as described herein mayresult in a change in one or more protein-protein interactions of theK-Ras, resulting in changes in cell growth, proliferation, or survival.

An amino acid residue in a protein “corresponds” to a given residue whenit occupies the same essential structural position within the protein asthe given residue. For example, a selected residue in a selected proteincorresponds to Gly 12 of Human K-Ras4A or Human K-Ras 4B or both whenthe selected residue occupies the same essential spatial or otherstructural relationship as Gly 12 in Human K-Ras4A or Human K-Ras 4B orboth. In some embodiments, where a selected protein is aligned formaximum homology with the Human K-Ras4A or Human K-Ras 4B protein, theposition in the aligned selected protein aligning with Gly 12 is said tocorrespond to Gly 12. Instead of a primary sequence alignment, a threedimensional structural alignment can also be used, e.g., where thestructure of the selected protein is aligned for maximum correspondencewith the Human K-Ras4A or Human K-Ras 4B protein and the overallstructures compared. In this case, an amino acid that occupies the sameessential position as Gly 12 in the structural model is said tocorrespond to the Gly 12 residue.

The terms “unsubstituted vinyl sulfone moiety”, “unsubstituted vinylsulfonamide moiety”, “unsubstituted fluoro(C₁-C₄)alkylketone moiety”,“unsubstituted chloro(C₁-C₄)alkylketone moiety”, “unsubstitutedacrylamide moiety”, “unsubstituted disulfide moiety”, “unsubstitutedthiol moiety”, “unsubstituted phosphonate moiety”, “unsubstitutedaldehyde moiety”, “unsubstituted enone moiety”, “unsubstituteddiazomethylketone moiety”, “unsubstituted diazomethylamide moiety”,“unsubstituted cyanocyclopropyl carboxamide moiety”, “unsubstitutedepoxide moiety”, “unsubstituted epoxyketone moiety”, “unsubstitutedepoxyamide moiety”, “unsubstituted aryl aldehyde moiety”, “unsubstitutedaryl dialdehyde moiety”, “unsubstituted dialdehyde moiety”,“unsubstituted nitrogen mustard moiety”, “unsubstituted propargylmoiety”, or “unsubstituted propargylamide moiety” are used according totheir plain ordinary chemical meaning and refer to those monovalentchemical groups named having the lowest molecular weight for each suchgroup while obeying the rules of chemical valency. A substituted form ofone of the named groups may be substituted with one or more of any ofthe substituent groups described herein while obeying the rules ofchemical valency.

“Switch 2,” as used herein, refers to a protein domain of a Ras protein(e.g. K-Ras) formed by residues corresponding to residues 60-76 of K-Ras(e.g. K-Ras Switch 2 refers to residues 60-76 of K-Ras). A “Switch 2Binding Region” is a region of a Ras protein (e.g. K-Ras) that is formedby amino acid residues that contact at least a portion of Switch 2 whenRas is bound to GTP. A “Switch 2—Binding Pocket” or “S2BP” is a cavitybound (the limits or boundaries of which are made), at least in part, bythe amino acid residues that form Switch 2 and the Switch 2 BindingRegion. In some embodiments, a “Switch 2—Binding Pocket” or “S2BP” is acavity, in the GDP bound form of Ras (e.g. K-Ras), bound (the limits orboundaries of which are made), at least in part, by the amino acidresidues that form Switch 2 and the Switch 2 Binding Region.

In some embodiments, the Switch 2—Binding Pocket is bound at least inpart by one or more of V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68,Y71, M72, Y96, Q99, and/or 1100 of K-Ras or equivalent residues inhomologous, related (e.g. H-Ras, N-Ras), or mutant Ras proteins. In someembodiments, the S2BP is bound at least in part by an amino acid residueshown to be interacting with the JO-01-189cbut compound in FIG. 4B orcontributing to the surface contacting the JO-01-189cbut compound inFIG. 4A. In some embodiments, the S2BP is bound at least in part by theleft portion of the proximity contour in FIG. 7 or 8. A compound asdescribed herein (including embodiments, examples, and compounds ofTable 1, 2, 3, 4, or 5), which binds to amino acids that form orcontacts amino acids that form the Switch 2—Binding Pocket is a “Switch2—Binding Pocket binding compound” and a moiety of a compound that bindsto amino acids that form or contacts amino acids that form the Switch2—Binding Pocket is a “Switch 2—Binding Pocket binding moiety”.

In some embodiments, a Switch 2—Binding Pocket binding compound orSwitch 2—Binding Pocket binding moiety binds or contacts one amino acidthat forms the Switch 2—Binding Pocket. In some embodiments, a Switch2—Binding Pocket binding compound or Switch 2—Binding Pocket bindingmoiety binds or contacts multiple amino acids that form the Switch2—Binding Pocket. In some embodiments, a Switch 2—Binding Pocket bindingcompound or Switch 2—Binding Pocket binding moiety binds or contacts oneK-Ras amino acid selected from V7, V9, G10, P34, T58, G60, Q61, E62,E63, R68, Y71, M72, Y96, Q99, and 1100. In some embodiments, a Switch2—Binding Pocket binding compound or Switch 2—Binding Pocket bindingmoiety binds or contacts multiple K-Ras amino acids selected from V7,V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and1100. In some embodiments, a Switch 2—Binding Pocket binding compound orSwitch 2—Binding Pocket binding moiety binds or contacts two K-Ras aminoacids selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71,M72, Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts three K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts four K-Ras amino acidsselected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72,Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts five K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts six K-Ras amino acidsselected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72,Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts seven K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts eight K-Ras aminoacids selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71,M72, Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts nine K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts ten K-Ras amino acidsselected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72,Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts eleven K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts twelve K-Ras aminoacids selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71,M72, Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts thirteen K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts fourteen K-Ras aminoacids selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71,M72, Y96, Q99, and 1100. In some embodiments, a Switch 2—Binding Pocketbinding compound or Switch 2—Binding Pocket binding moiety binds orcontacts fifteen K-Ras amino acids selected from V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100.

In some embodiments, a Switch 2—Binding Pocket binding compound orSwitch 2—Binding Pocket binding moiety binds or contacts one amino acidselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts multiple K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts two K-Ras amino acidsselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts three K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts four K-Ras amino acidsselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts five K-Ras amino acidsselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts six K-Ras amino acidsselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts seven K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts eight K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts nine K-Ras amino acidsselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts ten K-Ras amino acidsselected from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras),or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts eleven K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts twelve K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts thirteen K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts fourteen K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100. In someembodiments, a Switch 2—Binding Pocket binding compound or Switch2—Binding Pocket binding moiety binds or contacts fifteen K-Ras aminoacids selected from amino acids in a mutant K-Ras, related Ras (H-Ras,N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9, G10,P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100.

Compounds

In a first aspect is provided a compound which is capable of reactingwith an amino acid residue of a Ras protein (including K-Ras, N-Ras andH-Ras proteins). For example, the compound may contact a residue of aRas protein Switch 2 binding pocket. For example, where the residue ofthe Switch 2 binding pocket that contacts the compound may be V7, V9,G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, or 1100. Insome embodiments, the compound interacts with at least one of G60, E62,or E63.

In some embodiments, the compound covalently reacts with an amino acidresidue of the Ras protein to form a covalent bond (e.g. reversible orirreversible). For example the amino acid residue is a cysteine,aspartate, lysine, tyrosine or glutamate residue of the Ras protein. Insome embodiments, the amino acid residue is a cysteine residue, forexample a G12C or G13C residue of a K-Ras protein. In some embodiments,the amino acid residue is an aspartate residue, for example a G12D orG13D residue of a K-Ras protein.

In some embodiments, a compound having the formula R¹-L¹-L²-L³-E isprovided. R¹ is a Switch 2—Binding Pocket binding moiety. L¹ is a bondor a divalent radical chemical linker. L² is a bond or a divalentradical chemical linker. L³ is a bond or a divalent radical chemicallinker. E is an electrophilic chemical moiety capable of forming acovalent bond with a Ras cysteine residue or a Ras aspartate residue. Insome embodiments, Ras is a K-Ras. In some embodiments, the compoundcontacts a residue of K-Ras Switch 2. In some embodiments, wherein thecompound contacts K-Ras, R¹ contacts V7, V9, G10, P34, T58, G60, Q61,E62, E63, R68, Y71, M72, Y96, Q99, or 1100. For example, R¹ contacts atleast one of G60, E62, or E63. In some embodiments, the compound doesnot contact the residues of K-Ras that contact GTP. In some embodiments,the compound does not contact the residues of K-Ras that contact theguanine of GTP or GDP. In some embodiments, the compound does notcontact the residues of K-Ras that contact GDP. In some embodiments, thecompound forms an irreversible covalent bond with a K-Ras cysteineresidue. In some embodiments, the compound forms a reversible covalentbond with a K-Ras cysteine residue. In some embodiments, the compoundforms an irreversible covalent bond with a K-Ras aspartate residue. Insome embodiments, the compound forms a reversible covalent bond with aK-Ras aspartate residue. In some embodiments, R¹ contacts residues thatcontact Switch 2 in the GTP bound form of K-Ras. In some embodiments, R¹contacts residues that contact Switch 2 in the GDP bound form of K-Ras.In some embodiments, R¹ is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. Insome embodiments, R¹ is substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl. In someembodiments, R¹ is substituted or unsubstituted aryl or substituted orunsubstituted heteroaryl. In some embodiments, R¹ is R³-substituted orunsubstituted aryl or R³⁻-substituted or unsubstituted heteroaryl. Insome embodiments, R¹ is R³-substituted or unsubstituted fused ring aryl.In some embodiments, R¹ is R³-substituted or unsubstituted fused ringheteroaryl.

In some embodiments, R¹ is

In some embodiments R¹ is R³-substituted pyridinyl, R³-substitutedpyrimidinyl, R³-substituted thiophenyl, R³-substituted furanyl,R³-substituted indolyl, R³-substituted benzoxadiazolyl, R³-substitutedbenzodioxolyl, R³-substituted benzodioxanyl, R³-substitutedthianaphthanyl, R³-substituted pyrrolopyridinyl, R³-substitutedindazolyl, R³-substituted quinolinyl, R³-substituted quinoxalinyl,R³-substituted pyridopyrazinyl, R³-substituted quinazolinonyl,R³-substituted benzoisoxazolyl, R³-substituted imidazopyridinyl,R³-substituted benzofuranyl, R³-substituted benzothiophenyl,R³-substituted phenyl, R³-substituted naphthyl, R³-substituted biphenyl,R³-substituted pyrrolyl, R³-substituted pyrazolyl, R³-substitutedimidazolyl, R³-substituted pyrazinyl, R³-substituted oxazolyl,R³-substituted isoxazolyl, R³-substituted thiazolyl, R³-substitutedfurylthienyl, R³-substituted pyridyl, R³-substituted pyrimidyl,R³-substituted benzothiazolyl, R³-substituted purinyl, R³-substitutedbenzimidazolyl, R³-substituted isoquinolyl, R³-substituted thiadiazolyl,R³-substituted oxadiazolyl, R³-substituted pyrrolyl, R³-substituteddiazolyl, R³-substituted triazolyl, R³-substituted tetrazolyl,R³-substituted benzothiadiazolyl, R³-substituted isothiazolyl,R³-substituted pyrazolopyrimidinyl, R³-substituted pyrrolopyrimidinyl,R³-substituted benzotriazolyl, or R³-substituted quinolyl. In someembodiments R¹ is substituted pyridinyl, substituted pyrimidinyl,substituted thiophenyl, substituted furanyl, substituted indolyl,substituted benzoxadiazolyl, substituted benzodioxolyl, substitutedbenzodioxanyl, substituted thianaphthanyl, substituted pyrrolopyridinyl,substituted indazolyl, substituted quinolinyl, substituted quinoxalinyl,substituted pyridopyrazinyl, substituted quinazolinonyl, substitutedbenzoisoxazolyl, substituted imidazopyridinyl, substituted benzofuranyl,substituted benzothiophenyl, substituted phenyl, substituted naphthyl,substituted biphenyl, substituted pyrrolyl, substituted pyrazolyl,substituted imidazolyl, substituted pyrazinyl, substituted oxazolyl,substituted isoxazolyl, substituted thiazolyl, substituted furylthienyl,substituted pyridyl, substituted pyrimidyl, substituted benzothiazolyl,substituted purinyl, substituted benzimidazolyl, substitutedisoquinolyl, substituted thiadiazolyl, substituted oxadiazolyl,substituted pyrrolyl, substituted diazolyl, substituted triazolyl,substituted tetrazolyl, substituted benzothiadiazolyl, substitutedisothiazolyl, substituted pyrazolopyrimidinyl, substitutedpyrrolopyrimidinyl, substituted benzotriazolyl, or substituted quinolyl.

In some embodiments R¹ is unsubstituted pyridinyl, unsubstitutedpyrimidinyl, unsubstituted thiophenyl, unsubstituted furanyl,unsubstituted indolyl, unsubstituted benzoxadiazolyl, unsubstitutedbenzodioxolyl, unsubstituted benzodioxanyl, unsubstitutedthianaphthanyl, unsubstituted pyrrolopyridinyl, unsubstituted indazolyl,unsubstituted quinolinyl, unsubstituted quinoxalinyl, unsubstitutedpyridopyrazinyl, unsubstituted quinazolinonyl, unsubstitutedbenzoisoxazolyl, unsubstituted imidazopyridinyl, unsubstitutedbenzofuranyl, unsubstituted benzothiophenyl, unsubstituted phenyl,unsubstituted naphthyl, unsubstituted biphenyl, unsubstituted pyrrolyl,unsubstituted pyrazolyl, unsubstituted imidazolyl, unsubstitutedpyrazinyl, unsubstituted oxazolyl, unsubstituted isoxazolyl,unsubstituted thiazolyl, unsubstituted furylthienyl, unsubstitutedpyridyl, unsubstituted pyrimidyl, unsubstituted benzothiazolyl,unsubstituted purinyl, unsubstituted benzimidazolyl, unsubstitutedisoquinolyl, unsubstituted thiadiazolyl, unsubstituted oxadiazolyl,unsubstituted pyrrolyl, unsubstituted diazolyl, unsubstituted triazolyl,unsubstituted tetrazolyl, unsubstituted benzothiadiazolyl, unsubstitutedisothiazolyl, unsubstituted pyrazolopyrimidinyl, unsubstitutedpyrrolopyrimidinyl, unsubstituted benzotriazolyl, or unsubstitutedquinolyl.

R³ is independently hydrogen, oxo, halogen, —CX₃, —CN, —SO₂Cl,—SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂, —NHC═(O)NR′R⁸,—N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰,—NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl. In some embodiments, R³ is independentlyhydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl. Twoadjacent R³ substituents may optionally be joined to form a substitutedor unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl. Two R³ substituents bonded to the same atommay optionally be joined to form a substituted or unsubstitutedcycloalkyl or substituted or unsubstituted heterocycloalkyl. In someembodiments, R³ is methyl, —Cl, —NH₂, —I, —CCH, —CH₂CH₂OH, —OCH₂CCH,—CF₃, —OCH₃, —OH, —CH₂CH₃, —NHS(O)₂CH₃, —CH₂NH₂, —Br, isoxazolyl,—NHC(O)OC(CH₃)₃, p-chlorophenyl, thiophenyl, —F, pyrazolyl, —CH₂OH,—C(O)NHCH₂CH₂OH, —OCH₂CH₂OH, —S(O)₂NH₂, tetrazolyl, —CHCH₃OH, —C(O)CH₃,—C(O)H, —OCH₃, —C(O)OH, —C(O)OCH₃, —C(O)NH₂, —N(CH₃)₂, —CH₂NH₂,—CH₂NHC(O) CH₃, pyrrolidinyl, —OCH₂CH₂NH₂, —C(O)N(CH₃)₂, NHCH₃,—NHC(O)CH₃, —CN, —C(O)OCH₃, or

R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen, halogen, —CF₃, —CN, —OH,—NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH,—NHOH, —OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl. In someembodiments, R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen, substitutedor unsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl. R⁷ and R⁸ substituents bonded to the samenitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl.

The symbol m is independently 1 or 2. The symbol v is independently 1 or2. The symbol n is independently an integer from 0 to 4. The symbol X isindependently —Cl, —Br, —I, or —F. In some embodiments v is 1. In otherembodiments, v is 2. In some embodiments m is 1. In some embodiments mis 2. In some embodiments n is 0. In some embodiments n is 1. In someembodiments n is 2. In some embodiments n is 3. In some embodiments n is4. In some embodiments, X is —Cl. In some embodiments, X is —Br. In someembodiments, X is —I. In some embodiments, X is —F.

The symbol e2 is independently an integer from 0 to 2. The symbol e3 isindependently an integer from 0 to 3. The symbol e4 is independently aninteger from 0 to 4. The symbol e5 is independently an integer from 0 to5. The symbol e6 is independently an integer from 0 to 6. The symbol e7is independently an integer from 0 to 7. The symbol f2 is independentlyan integer from 0 to 2. The symbol f6 is independently an integer from 0to 6. The symbol f7 is independently an integer from 0 to 7. The symbolf8 is independently an integer from 0 to 8. The symbol f9 isindependently an integer from 0 to 9. The symbol f10 is independently aninteger from 0 to 10. The symbol f12 is independently an integer from 0to 12. The symbol f14 is independently an integer from 0 to 14.

L¹, L² and L³ are independently a bond, —NR^(2C)—, —O—, —S—, —C(O)—,—S(O)—, —S(O)₂—, substituted or unsubstituted alkylene, substituted orunsubstituted heteroalkylene, substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, substituted or unsubstitutedheteroarylene; or a substituted or unsubstituted spirocyclic linker. Insome embodiments, L¹ is a bond. In some embodiments, L² is a bond. Insome embodiments, L³ is a bond. In some embodiments, L¹ is substitutedor unsubstituted alkylene, substituted or unsubstituted heteroalkylene,substituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, substitutedor unsubstituted heteroarylene; or a substituted or unsubstitutedspirocyclic linker. In some embodiments, L² is substituted orunsubstituted alkylene, substituted or unsubstituted heteroalkylene,substituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, substitutedor unsubstituted heteroarylene; or a substituted or unsubstitutedspirocyclic linker. In some embodiments, L³ is substituted orunsubstituted alkylene, substituted or unsubstituted heteroalkylene,substituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, substitutedor unsubstituted heteroarylene; or a substituted or unsubstitutedspirocyclic linker. In some embodiments, L¹ is —NR^(2C)—. In someembodiments, L¹ is —O—. In some embodiments, L¹ is —S—. In someembodiments, L¹ is —C(O)—. In some embodiments, L¹ is —S(O)—. In someembodiments, L¹ is —S(O)₂—. In some embodiments, L² is —NR^(2C-). Insome embodiments, L² is —O—. In some embodiments, L² is —S—. In someembodiments, L² is —C(O)—. In some embodiments, L² is —S(O)—. In someembodiments, L² is —S(O)₂—. In some embodiments, L³ is —NR^(2C)—. Insome embodiments, L³ is —O—. In some embodiments, L³ is —S—. In someembodiments, L³ is —C(O)—. In some embodiments, L³ is —S(O)—. In someembodiments, L³ is —S(O)₂—. In some embodiments, L¹ is independently—CR^(2A)R^(2B)—. In some embodiments, L² is independently—CR^(2A)R^(2B)—. In some embodiments, L³ is independently—CR^(2A)R^(2B)—. In some embodiments, L¹ is independently

In some embodiments, L² is independently

In some embodiments, L³ is independently

In some embodiments, L¹ is independently

In some embodiments, L² is independently

In some embodiments, L³ is independently

In some embodiments, L¹ is independently

In some embodiments, L² is independently

In some embodiments, L³ is independently

In some embodiments, L¹ is independently substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, substituted or unsubstitutedheteroarylene, or substituted or unsubstituted spirocyclic linker. Insome embodiments, L¹ is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C)-substituted or unsubstituted heteroarylene, or R^(2C)-substitutedor unsubstituted spirocyclic linker. In some embodiments, L¹ isindependently

In some embodiments, L² is independently substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, substituted or unsubstitutedheteroarylene, or substituted or unsubstituted spirocyclic linker. Insome embodiments, L² is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C)-substituted or unsubstituted heteroarylene, or R^(2C)-substitutedor unsubstituted spirocyclic linker. In some embodiments, L² isindependently

In some embodiments, L³ is independently substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, substituted or unsubstitutedheteroarylene, or substituted or unsubstituted spirocyclic linker. Insome embodiments, L³ is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C)-substituted or unsubstituted heteroarylene, or R^(2C)-substitutedor unsubstituted spirocyclic linker. In some embodiments, L³ isindependently

In some embodiments, L² is independently a bond, L³ is independently abond, and L¹ is

In some embodiments, L¹ is independently

In some embodiments, L² is independently

In some embodiments, L³ is independently

R^(2A) and R^(2B) are independently hydrogen, oxo, halogen, —CX^(a3),—CN, —SO₂Cl, —SO_(n1)R^(10a), —SO_(v1)NR^(7a)R^(8a), —NHNH₂,—ONR^(7a)R^(8a), —NHC═(O)NHNH₂, —NHC═(O)NR^(7a)R^(8a), —N(O)_(m1),—NR^(7a)R^(8a), —C(O)R^(9a), —C(O)—OR^(9a), —C(O)NR^(7a)R^(8a),—OR^(10a), —NR^(7a)SO₂R^(10a), —NR^(7a)C═(O)R^(9a),—NR^(7a)C(O)—OR^(9a), —NR^(7a)OR^(9a), —OCX^(a) ₃, —OCHX^(a) ₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. R^(2A) and R^(2B) substituentsbonded to the same atom may optionally be joined to form a substitutedor unsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl. In some embodiments, R^(2A) is independently hydrogen,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. In some embodiments, R^(2B) isindependently hydrogen, substituted or unsubstituted alkyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl.

R^(7a), R^(8a), R^(9a) and R^(10a) are independently hydrogen, halogen,—CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H,—SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl.R^(7a) and R^(8a) substituents bonded to the same nitrogen atom mayoptionally be joined to form a substituted or unsubstitutedheterocycloalkyl or substituted or unsubstituted heteroaryl. In someembodiments, R^(7a), R^(8a), R^(9a) and R^(10a) are independentlyhydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl.

R^(2C) is independently hydrogen, oxo, halogen, —CX^(c) ₃, —CN, —SO₂Cl,—SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c), —NHNH₂, —ONR^(7c)R^(8c),—NHC═(O)NHNH₂, —NHC═(O)NR^(7c)R^(8c), —N(O)_(m3), —NR^(7c)R^(8c),—C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c), —OR^(10c),—NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c), —NR^(7c)C(O)—OR^(9c),—NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl. Two adjacent R^(2C) substituents may optionally be joined toform a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. Two R^(2C) substituents bondedto the same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl. In some embodiments, R^(2C) is independently hydrogen,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl.

R^(7c), R^(8c), R^(9c) and R^(10c) are independently hydrogen, halogen,—CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H,—SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl.R^(7c) and R^(8c) substituents bonded to the same nitrogen atom mayoptionally be joined to form a substituted or unsubstitutedheterocycloalkyl or substituted or unsubstituted heteroaryl. In someembodiments, R^(7c), R^(8c), R^(9c) and R^(10c) are independentlyhydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl.

The symbols m1, m3, v1, and v3 are independently an integer from 1 to 2.The symbols n1 and n3 are independently an integer from 0 to 4. Thesymbols X^(a) and X^(c) are independently —Cl, —Br, —I, or —F. Thesymbol v1 is independently 1 or 2. In some embodiments, v1 is 1. In someembodiments, v1 is 2. The symbol m1 is independently an integer from 1to 2. In some embodiments, m1 is 1. In some embodiments, m1 is 2. Thesymbol n1 is independently an integer from 0 to 4. In some embodiments,n1 is 0. In some embodiments, n1 is 1. In some embodiments, n1 is 2. Insome embodiments, n1 is 3. In some embodiments, n1 is 4. X^(a) isindependently —Cl, —Br, —I, or —F. In some embodiments, X^(a) is —Cl. Insome embodiments, X^(a) is —Br. In some embodiments, X^(a) is —I. Insome embodiments, X^(a) is —F. The symbol v3 is independently 1 or 2. Insome embodiments, v3 is 1. In some embodiments, v3 is 2. The symbol m3is independently an integer from 1 to 2. In some embodiments, m3 is 1.In some embodiments, m3 is 2. The symbol n3 is independently an integerfrom 0 to 4. In some embodiments, n3 is 0. In some embodiments, n3 is 1.In some embodiments, n3 is 2. In some embodiments, n3 is 3. In someembodiments, n3 is 4. X^(c) is independently —Cl, —Br, —I, or —F. Insome embodiments, X^(c) is —Cl. In some embodiments, X^(c) is —Br. Insome embodiments, X^(c) is —I. In some embodiments, X^(c) is —F. Thesymbol z is independently an integer from 0 to 10. In some embodiments,z is 0. In some embodiments, z is 1. In some embodiments, z is 2. Insome embodiments, z is 3. In some embodiments, z is 4. In someembodiments, z is 5. In some embodiments, z is 6. In some embodiments, zis 7. In some embodiments, z is 8. In some embodiments, z is 9. In someembodiments, z is 10.

In some embodiments, E is an electrophilic chemical moiety capable offorming a covalent bond with a K-Ras cysteine residue. In someembodiments, E is an electrophilic chemical moiety capable of forming acovalent bond with a K-Ras aspartate residue. In some embodiments, E isan electrophilic chemical moiety capable of forming a covalent bond witha K-Ras cysteine sidechain. In some embodiments, E is an electrophilicchemical moiety capable of forming a covalent bond with a K-Rasaspartate sidechain. In some embodiments, E is an electrophilic chemicalmoiety capable of forming a covalent bond with a K-Ras cysteine sulfur.In some embodiments, E is an electrophilic chemical moiety capable offorming a covalent bond with a K-Ras aspartate sidechain oxygen. In someembodiments, E is an electrophilic chemical moiety capable of forming acovalent bond with a K-Ras residue 12 cysteine. In some embodiments, Eis an electrophilic chemical moiety capable of forming a covalent bondwith a K-Ras residue 12 asparate. In some embodiments, E is anelectrophilic chemical moiety capable of forming a covalent bond with aK-Ras residue 13 cysteine. In some embodiments, E is an electrophilicchemical moiety capable of forming a covalent bond with a K-Ras residue13 asparate. In some embodiments, E is an electrophilic chemical moietycapable of forming a covalent bond with a K-Ras residue near the Switch2—Binding Pocket in the folded protein. In some embodiments, E is anelectrophilic chemical moiety capable of forming a covalent bond with aK-Ras residue in the Switch 2—Binding Pocket in the folded protein. Insome embodiments, E is an electrophilic chemical moiety capable offorming an irreversible covalent bond with a K-Ras residue. In someembodiments, E is an electrophilic chemical moiety capable of forming areversible covalent bond with a K-Ras residue.

In some embodiments, E comprises a substituted or unsubstituted vinylsulfone moiety, substituted or unsubstituted vinyl sulfonamide moiety,substituted or unsubstituted fluoro(C₁-C₄)alkylketone moiety,substituted or unsubstituted chloro(C₁-C₄)alkylketone moiety,substituted or unsubstituted acrylamide moiety, substituted orunsubstituted disulfide moiety, substituted or unsubstituted thiolmoiety, substituted or unsubstituted phosphonate moiety, substituted orunsubstituted aldehyde moiety, substituted or unsubstituted enonemoiety, substituted or unsubstituted diazomethylketone moiety,substituted or unsubstituted diazomethylamide moiety, substituted orunsubstituted cyanocyclopropyl carboxamide moiety, substituted orunsubstituted epoxide moiety, substituted or unsubstituted epoxyketonemoiety, substituted or unsubstituted epoxyamide moiety, substituted orunsubstituted aryl aldehyde moiety, substituted or unsubstituted aryldialdehyde moiety, substituted or unsubstituted dialdehyde moiety,substituted or unsubstituted nitrogen mustard moiety, substituted orunsubstituted propargyl moiety, substituted or unsubstitutedpropargylamide moiety,

In some embodiments, E is a substituted or unsubstituted vinyl sulfonemoiety, substituted or unsubstituted vinyl sulfonamide moiety,substituted or unsubstituted fluoro(C₁-C₄)alkylketone moiety,substituted or unsubstituted chloro(C₁-C₄)alkylketone moiety,substituted or unsubstituted acrylamide moiety, substituted orunsubstituted disulfide moiety, substituted or unsubstituted thiolmoiety, substituted or unsubstituted phosphonate moiety, substituted orunsubstituted aldehyde moiety, substituted or unsubstituted enonemoiety, substituted or unsubstituted diazomethylketone moiety,substituted or unsubstituted diazomethylamide moiety, substituted orunsubstituted cyanocyclopropyl carboxamide moiety, substituted orunsubstituted epoxide moiety, substituted or unsubstituted epoxyketonemoiety, substituted or unsubstituted epoxyamide moiety, substituted orunsubstituted aryl aldehyde moiety, substituted or unsubstituted aryldialdehyde moiety, substituted or unsubstituted dialdehyde moiety,substituted or unsubstituted nitrogen mustard moiety, substituted orunsubstituted propargyl moiety, substituted or unsubstitutedpropargylamide moiety,

In some embodiments, E comprises an unsubstituted vinyl sulfone moiety,unsubstituted vinyl sulfonamide moiety, unsubstitutedfluoro(C₁-C₄)alkylketone moiety, unsubstituted chloro(C1-C₄)alkylketonemoiety, unsubstituted acrylamide moiety, unsubstituted disulfide moiety,unsubstituted thiol moiety, unsubstituted phosphonate moiety,unsubstituted aldehyde moiety, unsubstituted enone moiety, unsubstituteddiazomethylketone moiety, unsubstituted diazomethylamide moiety,unsubstituted cyanocyclopropyl carboxamide moiety, unsubstituted epoxidemoiety, unsubstituted epoxyketone moiety, unsubstituted epoxyamidemoiety, unsubstituted aryl aldehyde moiety, unsubstituted aryldialdehyde moiety, unsubstituted dialdehyde moiety, unsubstitutednitrogen mustard moiety, unsubstituted propargyl moiety, orunsubstituted propargylamide moiety. In some embodiments, E is anunsubstituted vinyl sulfone moiety, unsubstituted vinyl sulfonamidemoiety, unsubstituted fluoro(C₁-C₄)alkylketone moiety, unsubstitutedchloro(C₁-C₄)alkylketone moiety, unsubstituted acrylamide moiety,unsubstituted disulfide moiety, unsubstituted thiol moiety,unsubstituted phosphonate moiety, unsubstituted aldehyde moiety,unsubstituted enone moiety, unsubstituted diazomethylketone moiety,unsubstituted diazomethylamide moiety, unsubstituted cyanocyclopropylcarboxamide moiety, unsubstituted epoxide moiety, unsubstitutedepoxyketone moiety, unsubstituted epoxyamide moiety, unsubstituted arylaldehyde moiety, unsubstituted aryl dialdehyde moiety, unsubstituteddialdehyde moiety, unsubstituted nitrogen mustard moiety, unsubstitutedpropargyl moiety, or unsubstituted propargylamide moiety.

R¹³ is independently hydrogen, oxo, halogen, —CX^(b) ₃, —CN, —SO₂Cl,—SO_(r)R¹⁷, —SO_(p)NR¹⁴R¹⁵, —NHNH₂, —ONR¹⁴R¹⁵, —NHC═(O)NHNH₂,—NHC(O)NR¹⁴R¹⁵, —N(O)_(q), —NR¹⁴R¹⁵, —C(O)R¹⁶, —C(O)—OR¹⁶, —C(O)NR¹⁴R¹⁵,—OR¹⁷, —NR¹⁴SO₂R¹⁷, —NR¹⁴C═(O)R¹⁶, —NR¹⁴C(O)—OR¹⁶, —NR¹⁴OR¹⁶, —OCX^(b)₃, —OCHX^(b) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl. Twoadjacent R¹³ substituents may optionally be joined to form a substitutedor unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl. Two R¹³ substituents bonded to the same atommay optionally be joined to form a substituted or unsubstitutedcycloalkyl or substituted or unsubstituted heterocycloalkyl. In someembodiments, R¹³ is hydrogen. In some embodiments, R¹³ is methyl. Insome embodiments, R¹³ is ethyl. In some embodiments, R¹³ is —CN. In someembodiments, R¹³ is —NO₂.

R¹⁴, R¹⁵, R¹⁶, and R¹⁷ are independently hydrogen, halogen, —CF₃, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl. R¹⁴and R¹⁵ substituents bonded to the same nitrogen atom may optionally bejoined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl. In some embodiments, R¹⁴, R¹⁵,R¹⁶, and R¹⁷ are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl. The symbol p is independently 1 or 2. In some embodiments, pis 1. In some embodiments, p is 2. The symbol q is independently aninteger from 1 to 2. In some embodiments, q is 1. In some embodiments, qis 2. The symbol r is independently an integer from 0 to 4. In someembodiments, r is 0. In some embodiments, r is 1. In some embodiments, ris 2. In some embodiments, r is 3. In some embodiments, r is 4. X^(b) isindependently —Cl, —Br, —I, or —F. In some embodiments, X^(b) is —Cl. Insome embodiments, X^(b) is —Br. In some embodiments, X^(b) is —I. Insome embodiments, X^(b) is —F.

In some embodiments of the compounds provided herein, R¹ isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R²⁰-substituted or unsubstituted alkyl, R²⁰-substitutedor unsubstituted heteroalkyl, R²⁰-substituted or unsubstitutedcycloalkyl, R²⁰-substituted or unsubstituted heterocycloalkyl,R²⁰-substituted or unsubstituted aryl, or R²⁰-substituted orunsubstituted heteroaryl.

R²⁰ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R²¹-substituted or unsubstituted alkyl, R²¹-substituted or unsubstitutedheteroalkyl, R²¹-substituted or unsubstituted cycloalkyl,R²¹-substituted or unsubstituted heterocycloalkyl, R²¹-substituted orunsubstituted aryl, or R²¹-substituted or unsubstituted heteroaryl.

R²¹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R²²-substituted or unsubstituted alkyl, R²²-substituted or unsubstitutedheteroalkyl, R²²-substituted or unsubstituted cycloalkyl,R²²-substituted or unsubstituted heterocycloalkyl, R²²-substituted orunsubstituted aryl, or R²²-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R² isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R²³-substituted or unsubstituted alkyl, R²³-substitutedor unsubstituted heteroalkyl, R²³-substituted or unsubstitutedcycloalkyl, R²³-substituted or unsubstituted heterocycloalkyl,R²³-substituted or unsubstituted aryl, or R²³-substituted orunsubstituted heteroaryl.

R²³ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R²⁴-substituted or unsubstituted alkyl, R²⁴-substituted or unsubstitutedheteroalkyl, R²⁴-substituted or unsubstituted cycloalkyl,R²⁴-substituted or unsubstituted heterocycloalkyl, R²⁴-substituted orunsubstituted aryl, or R²⁴-substituted or unsubstituted heteroaryl.

R²⁴ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R²⁵-substituted or unsubstituted alkyl, R²⁵-substituted or unsubstitutedheteroalkyl, R²⁵-substituted or unsubstituted cycloalkyl,R²⁵-substituted or unsubstituted heterocycloalkyl, R²⁵-substituted orunsubstituted aryl, or R²⁵-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(2A) isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(23A)-substituted or unsubstituted alkyl,R^(23A)-substituted or unsubstituted heteroalkyl, R^(23A)-substituted orunsubstituted cycloalkyl, R^(23A)-substituted or unsubstitutedheterocycloalkyl, R^(23A)-substituted or unsubstituted aryl, orR^(23A)-substituted or unsubstituted heteroaryl.

R^(23A) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(24A)-substituted or unsubstituted alkyl,R^(24A)-substituted or unsubstituted heteroalkyl, R^(24A)-substituted orunsubstituted cycloalkyl, R^(24A)-substituted or unsubstitutedheterocycloalkyl, R^(24A)-substituted or unsubstituted aryl, orR^(24A)-substituted or unsubstituted heteroaryl.

R^(24A) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(25A)-substituted or unsubstituted alkyl,R^(25A)-substituted or unsubstituted heteroalkyl, R^(25A)-substituted orunsubstituted cycloalkyl, R^(25A)-substituted or unsubstitutedheterocycloalkyl, R^(25A)-substituted or unsubstituted aryl, orR^(25A)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(2B) isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(23B)-substituted or unsubstituted alkyl,R^(23B)-substituted or unsubstituted heteroalkyl, R^(23B)-substituted orunsubstituted cycloalkyl, R^(23B)-substituted or unsubstitutedheterocycloalkyl, R^(23B)-substituted or unsubstituted aryl, orR^(23B)-substituted or unsubstituted heteroaryl.

R^(23B) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(24B)-substituted or unsubstituted alkyl,R^(24B)-substituted or unsubstituted heteroalkyl, R^(24B)-substituted orunsubstituted cycloalkyl, R^(24B)-substituted or unsubstitutedheterocycloalkyl, R^(24B)-substituted or unsubstituted aryl, orR^(24B)-substituted or unsubstituted heteroaryl.

R^(24B) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(25B)-substituted or unsubstituted alkyl,R^(25B)-substituted or unsubstituted heteroalkyl, R^(25B)-substituted orunsubstituted cycloalkyl, R^(25B)-substituted or unsubstitutedheterocycloalkyl, R^(25B)-substituted or unsubstituted aryl, orR^(25B)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(2C) isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(23C)-substituted or unsubstituted alkyl,R^(23C)-substituted or unsubstituted heteroalkyl, R^(23C)-substituted orunsubstituted cycloalkyl, R^(23C)-substituted or unsubstitutedheterocycloalkyl, R^(23C)-substituted or unsubstituted aryl, orR^(23C)-substituted or unsubstituted heteroaryl.

R^(23C) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(24C)-substituted or unsubstituted alkyl,R^(24C)-substituted or unsubstituted heteroalkyl, R^(24C)-substituted orunsubstituted cycloalkyl, R^(24C)-substituted or unsubstitutedheterocycloalkyl, R^(24C)-substituted or unsubstituted aryl, orR^(24C)-substituted or unsubstituted heteroaryl.

R^(24C) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(25C)-substituted or unsubstituted alkyl,R^(25C)-substituted or unsubstituted heteroalkyl, R^(25C)-substituted orunsubstituted cycloalkyl, R^(25C)-substituted or unsubstitutedheterocycloalkyl, R^(25C)-substituted or unsubstituted aryl, orR^(25C)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R³ isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R²⁶-substituted or unsubstituted alkyl, R²⁶-substitutedor unsubstituted heteroalkyl, R²⁶-substituted or unsubstitutedcycloalkyl, R²⁶-substituted or unsubstituted heterocycloalkyl,R²⁶-substituted or unsubstituted aryl, or R²⁶-substituted orunsubstituted heteroaryl.

R²⁶ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R²⁷-substituted or unsubstituted alkyl, R²⁷-substituted or unsubstitutedheteroalkyl, R²⁷-substituted or unsubstituted cycloalkyl,R²⁷-substituted or unsubstituted heterocycloalkyl, R²⁷-substituted orunsubstituted aryl, or R²⁷-substituted or unsubstituted heteroaryl.

R²⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R²⁸-substituted or unsubstituted alkyl, R²⁸-substituted or unsubstitutedheteroalkyl, R²⁸-substituted or unsubstituted cycloalkyl,R²⁸-substituted or unsubstituted heterocycloalkyl, R²⁸-substituted orunsubstituted aryl, or R²⁸-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, L¹ isindependently a bond, —NH—, —O—, —S—, —C(O)—, —S(O)—, —S(O)₂—,R²⁹-substituted or unsubstituted alkylene, R²⁹-substituted orunsubstituted heteroalkylene, R²⁹-substituted or unsubstitutedcycloalkylene, R²⁹-substituted or unsubstituted heterocycloalkylene,R²⁹-substituted or unsubstituted arylene, or R²⁹-substituted orunsubstituted heteroarylene.

R²⁹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁰-substituted or unsubstituted alkyl, R³⁰-substituted or unsubstitutedheteroalkyl, R³⁰-substituted or unsubstituted cycloalkyl,R³⁰-substituted or unsubstituted heterocycloalkyl, R³⁰-substituted orunsubstituted aryl, or R³⁰-substituted or unsubstituted heteroaryl.

R³⁰ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³¹-substituted or unsubstituted alkyl, R³¹-substituted or unsubstitutedheteroalkyl, R³¹-substituted or unsubstituted cycloalkyl,R³¹-substituted or unsubstituted heterocycloalkyl, R³¹-substituted orunsubstituted aryl, or R³¹-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, L² isindependently a bond, —NH—, —O—, —S—, —C(O)—, —S(O)—, —S(O)₂—,R³²-substituted or unsubstituted alkylene, R³²-substituted orunsubstituted heteroalkylene, R³²-substituted or unsubstitutedcycloalkylene, R³²-substituted or unsubstituted heterocycloalkylene,R³²-substituted or unsubstituted arylene, or R³²-substituted orunsubstituted heteroarylene.

R³² is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³³-substituted or unsubstituted alkyl, R³³-substituted or unsubstitutedheteroalkyl, R³³-substituted or unsubstituted cycloalkyl,R³³-substituted or unsubstituted heterocycloalkyl, R³³-substituted orunsubstituted aryl, or R³³-substituted or unsubstituted heteroaryl.

R³³ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁴-substituted or unsubstituted alkyl, R³⁴-substituted or unsubstitutedheteroalkyl, R³⁴-substituted or unsubstituted cycloalkyl,R³⁴-substituted or unsubstituted heterocycloalkyl, R³⁴-substituted orunsubstituted aryl, or R³⁴-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, L³ isindependently a bond, —NH—, —O—, —S—, —C(O)—, —S(O)—, —S(O)₂—,R³⁵-substituted or unsubstituted alkylene, R³⁵-substituted orunsubstituted heteroalkylene, R³⁵-substituted or unsubstitutedcycloalkylene, R³⁵-substituted or unsubstituted heterocycloalkylene,R³⁵-substituted or unsubstituted arylene, or R³⁵-substituted orunsubstituted heteroarylene.

R³⁵ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁶-substituted or unsubstituted alkyl, R³⁶-substituted or unsubstitutedheteroalkyl, R³⁶-substituted or unsubstituted cycloalkyl,R³⁶-substituted or unsubstituted heterocycloalkyl, R³⁶-substituted orunsubstituted aryl, or R³⁶-substituted or unsubstituted heteroaryl.

R³⁶ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁷-substituted or unsubstituted alkyl, R³⁷-substituted or unsubstitutedheteroalkyl, R³⁷-substituted or unsubstituted cycloalkyl,R³⁷-substituted or unsubstituted heterocycloalkyl, R³⁷-substituted orunsubstituted aryl, or R³⁷-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R⁷ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R³⁸-substituted or unsubstituted alkyl, R³⁸-substituted or unsubstitutedheteroalkyl, R³⁸-substituted or unsubstituted cycloalkyl,R³⁸-substituted or unsubstituted heterocycloalkyl, R³⁸-substituted orunsubstituted aryl, or R³⁸-substituted or unsubstituted heteroaryl.

R³⁸ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,—S(O)₂CHCH₂, —NHS(O)₂CHCH₂, R³⁹-substituted or unsubstituted alkyl,R³⁹-substituted or unsubstituted heteroalkyl, R³⁹-substituted orunsubstituted cycloalkyl, R³⁹-substituted or unsubstitutedheterocycloalkyl, R³⁹-substituted or unsubstituted aryl, orR³⁹-substituted or unsubstituted heteroaryl.

R³⁹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,—S(O)₂CHCH₂, —NHS(O)₂CHCH₂, R⁴⁰-substituted or unsubstituted alkyl,R⁴⁰-substituted or unsubstituted heteroalkyl, R⁴⁰-substituted orunsubstituted cycloalkyl, R⁴⁰-substituted or unsubstitutedheterocycloalkyl, R⁴⁰-substituted or unsubstituted aryl, orR⁴⁰-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R⁸ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴¹-substituted or unsubstituted alkyl, R⁴¹-substituted or unsubstitutedheteroalkyl, R⁴¹-substituted or unsubstituted cycloalkyl,R⁴¹-substituted or unsubstituted heterocycloalkyl, R⁴¹-substituted orunsubstituted aryl, or R⁴¹-substituted or unsubstituted heteroaryl.

R⁴¹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,—S(O)₂CHCH₂, —NHS(O)₂CHCH₂, R⁴²-substituted or unsubstituted alkyl,R⁴²-substituted or unsubstituted heteroalkyl, R⁴²-substituted orunsubstituted cycloalkyl, R⁴²-substituted or unsubstitutedheterocycloalkyl, R⁴²-substituted or unsubstituted aryl, orR⁴²-substituted or unsubstituted heteroaryl.

R⁴² is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,—S(O)₂CHCH₂, —NHS(O)₂CHCH₂, R⁴³-substituted or unsubstituted alkyl,R⁴³-substituted or unsubstituted heteroalkyl, R⁴³-substituted orunsubstituted cycloalkyl, R⁴³-substituted or unsubstitutedheterocycloalkyl, R⁴³-substituted or unsubstituted aryl, orR⁴³-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R⁹ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁴-substituted or unsubstituted alkyl, R⁴⁴-substituted or unsubstitutedheteroalkyl, R⁴⁴-substituted or unsubstituted cycloalkyl,R⁴⁴-substituted or unsubstituted heterocycloalkyl, R⁴⁴-substituted orunsubstituted aryl, or R⁴⁴-substituted or unsubstituted heteroaryl.

R⁴⁴ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁵-substituted or unsubstituted alkyl, R⁴⁵-substituted or unsubstitutedheteroalkyl, R⁴⁵-substituted or unsubstituted cycloalkyl,R⁴⁵-substituted or unsubstituted heterocycloalkyl, R⁴⁵-substituted orunsubstituted aryl, or R⁴⁵-substituted or unsubstituted heteroaryl.

R⁴⁵ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁶-substituted or unsubstituted alkyl, R⁴⁶-substituted or unsubstitutedheteroalkyl, R⁴⁶-substituted or unsubstituted cycloalkyl,R⁴⁶-substituted or unsubstituted heterocycloalkyl, R⁴⁶-substituted orunsubstituted aryl, or R⁴⁶-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R¹⁰ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁷-substituted or unsubstituted alkyl, R⁴⁷-substituted or unsubstitutedheteroalkyl, R⁴⁷-substituted or unsubstituted cycloalkyl,R⁴⁷-substituted or unsubstituted heterocycloalkyl, R⁴⁷-substituted orunsubstituted aryl, or R⁴⁷-substituted or unsubstituted heteroaryl.

R⁴⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁸-substituted or unsubstituted alkyl, R⁴⁸-substituted or unsubstitutedheteroalkyl, R⁴⁸-substituted or unsubstituted cycloalkyl,R⁴⁸-substituted or unsubstituted heterocycloalkyl, R⁴⁸-substituted orunsubstituted aryl, or R⁴⁸-substituted or unsubstituted heteroaryl.

R⁴⁸ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁴⁹-substituted or unsubstituted alkyl, R⁴⁹-substituted or unsubstitutedheteroalkyl, R⁴⁹-substituted or unsubstituted cycloalkyl,R⁴⁹-substituted or unsubstituted heterocycloalkyl, R⁴⁹-substituted orunsubstituted aryl, or R⁴⁹-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R¹³ isindependently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R⁵⁶-substituted or unsubstituted alkyl, R⁵⁶-substitutedor unsubstituted heteroalkyl, R⁵⁶-substituted or unsubstitutedcycloalkyl, R⁵⁶-substituted or unsubstituted heterocycloalkyl,R⁵⁶-substituted or unsubstituted aryl, or R⁵⁶-substituted orunsubstituted heteroaryl.

R⁵⁶ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁵⁷-substituted or unsubstituted alkyl, R⁵⁷-substituted or unsubstitutedheteroalkyl, R⁵⁷-substituted or unsubstituted cycloalkyl,R⁵⁷-substituted or unsubstituted heterocycloalkyl, R⁵⁷-substituted orunsubstituted aryl, or R⁵⁷-substituted or unsubstituted heteroaryl.

R⁵⁷ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁵⁸-substituted or unsubstituted alkyl, R⁵⁸-substituted or unsubstitutedheteroalkyl, R⁵⁸-substituted or unsubstituted cycloalkyl,R⁵⁸-substituted or unsubstituted heterocycloalkyl, R⁵⁸-substituted orunsubstituted aryl, or R⁵⁸-substituted or unsubstituted heteroaryl.

In another embodiment of the compounds provided herein, R¹⁴ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁵⁹-substituted or unsubstituted alkyl, R⁵⁹-substituted or unsubstitutedheteroalkyl, R⁵⁹-substituted or unsubstituted cycloalkyl,R⁵⁹-substituted or unsubstituted heterocycloalkyl, R⁵⁹-substituted orunsubstituted aryl, or R⁵⁹-substituted or unsubstituted heteroaryl.

R⁵⁹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁰-substituted or unsubstituted alkyl, R⁶⁰-substituted or unsubstitutedheteroalkyl, R⁶⁰-substituted or unsubstituted cycloalkyl,R⁶⁰-substituted or unsubstituted heterocycloalkyl, R⁶⁰-substituted orunsubstituted aryl, or R⁶⁰-substituted or unsubstituted heteroaryl.

R⁶⁰ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶¹-substituted or unsubstituted alkyl, R⁶¹-substituted or unsubstitutedheteroalkyl, R⁶¹-substituted or unsubstituted cycloalkyl,R⁶¹-substituted or unsubstituted heterocycloalkyl, R⁶¹-substituted orunsubstituted aryl, or R⁶¹-substituted or unsubstituted heteroaryl.

In a further embodiment of the compounds provided herein, R¹⁵ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶²-substituted or unsubstituted alkyl, R⁶²-substituted or unsubstitutedheteroalkyl, R⁶²-substituted or unsubstituted cycloalkyl,R⁶²-substituted or unsubstituted heterocycloalkyl, R⁶²-substituted orunsubstituted aryl, or R⁶²-substituted or unsubstituted heteroaryl.

R⁶² is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶³-substituted or unsubstituted alkyl, R⁶³-substituted or unsubstitutedheteroalkyl, R⁶³-substituted or unsubstituted cycloalkyl,R⁶³-substituted or unsubstituted heterocycloalkyl, R⁶³-substituted orunsubstituted aryl, or R⁶³-substituted or unsubstituted heteroaryl.

R⁶³ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁴-substituted or unsubstituted alkyl, R⁶⁴-substituted or unsubstitutedheteroalkyl, R⁶⁴-substituted or unsubstituted cycloalkyl,R⁶⁴-substituted or unsubstituted heterocycloalkyl, R⁶⁴-substituted orunsubstituted aryl, or R⁶⁴-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R¹⁶ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁵-substituted or unsubstituted alkyl, R⁶⁵-substituted or unsubstitutedheteroalkyl, R⁶⁵-substituted or unsubstituted cycloalkyl,R⁶⁵-substituted or unsubstituted heterocycloalkyl, R⁶⁵-substituted orunsubstituted aryl, or R⁶⁵-substituted or unsubstituted heteroaryl.

R⁶⁵ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁶-substituted or unsubstituted alkyl, R⁶⁶-substituted or unsubstitutedheteroalkyl, R⁶⁶-substituted or unsubstituted cycloalkyl,R⁶⁶-substituted or unsubstituted heterocycloalkyl, R⁶⁶-substituted orunsubstituted aryl, or R⁶⁶-substituted or unsubstituted heteroaryl.

R⁶⁶ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁷-substituted or unsubstituted alkyl, R⁶⁷-substituted or unsubstitutedheteroalkyl, R⁶⁷-substituted or unsubstituted cycloalkyl,R⁶⁷-substituted or unsubstituted heterocycloalkyl, R⁶⁷-substituted orunsubstituted aryl, or R⁶⁷-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R¹⁷ isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁸-substituted or unsubstituted alkyl, R⁶⁸-substituted or unsubstitutedheteroalkyl, R⁶⁸-substituted or unsubstituted cycloalkyl,R⁶⁸-substituted or unsubstituted heterocycloalkyl, R⁶⁸-substituted orunsubstituted aryl, or R⁶⁸-substituted or unsubstituted heteroaryl.

R⁶⁸ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁶⁹-substituted or unsubstituted alkyl, R⁶⁹-substituted or unsubstitutedheteroalkyl, R⁶⁹-substituted or unsubstituted cycloalkyl,R⁶⁹-substituted or unsubstituted heterocycloalkyl, R⁶⁹-substituted orunsubstituted aryl, or R⁶⁹-substituted or unsubstituted heteroaryl.

R⁶⁹ is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R⁷⁰-substituted or unsubstituted alkyl, R⁷⁰-substituted or unsubstitutedheteroalkyl, R⁷⁰-substituted or unsubstituted cycloalkyl,R⁷⁰-substituted or unsubstituted heterocycloalkyl, R⁷⁰-substituted orunsubstituted aryl, or R⁷⁰-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(7a) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(38a)-substituted or unsubstituted alkyl, R^(38a)-substituted orunsubstituted heteroalkyl, R^(38a)-substituted or unsubstitutedcycloalkyl, R^(38a)-substituted or unsubstituted heterocycloalkyl,R^(38a)-substituted or unsubstituted aryl, or R^(38a)-substituted orunsubstituted heteroaryl.

R^(38a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(39a)-substituted or unsubstituted alkyl,R^(39a)-substituted or unsubstituted heteroalkyl, R^(39a)-substituted orunsubstituted cycloalkyl, R^(39a)-substituted or unsubstitutedheterocycloalkyl, R^(39a)-substituted or unsubstituted aryl, orR^(39a)-substituted or unsubstituted heteroaryl.

R^(39a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(40a)-substituted or unsubstituted alkyl,R^(40a)-substituted or unsubstituted heteroalkyl, R^(40a)-substituted orunsubstituted cycloalkyl, R^(40a)-substituted or unsubstitutedheterocycloalkyl, R^(40a)-substituted or unsubstituted aryl, orR^(40a)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(8a) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(41a)-substituted or unsubstituted alkyl, R^(41a)-substituted orunsubstituted heteroalkyl, R^(41a)-substituted or unsubstitutedcycloalkyl, R^(41a)-substituted or unsubstituted heterocycloalkyl,R^(41a)-substituted or unsubstituted aryl, or R^(41a)-substituted orunsubstituted heteroaryl.

R^(41a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(42a)-substituted or unsubstituted alkyl,R^(42a)-substituted or unsubstituted heteroalkyl, R^(42a)-substituted orunsubstituted cycloalkyl, R^(42a)-substituted or unsubstitutedheterocycloalkyl, R^(42a)-substituted or unsubstituted aryl, orR^(42a)-substituted or unsubstituted heteroaryl.

R^(42a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(43a)-substituted or unsubstituted alkyl,R^(43a)-substituted or unsubstituted heteroalkyl, R^(43a)-substituted orunsubstituted cycloalkyl, R^(43a)-substituted or unsubstitutedheterocycloalkyl, R^(43a)-substituted or unsubstituted aryl, orR^(43a)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(9a) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(44a)-substituted or unsubstituted alkyl, R^(44a)-substituted orunsubstituted heteroalkyl, R^(44a)-substituted or unsubstitutedcycloalkyl, R^(44a)-substituted or unsubstituted heterocycloalkyl,R^(44a)-substituted or unsubstituted aryl, or R^(44a)-substituted orunsubstituted heteroaryl.

R^(44a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(45a)-substituted or unsubstituted alkyl,R^(45a)-substituted or unsubstituted heteroalkyl, R^(45a)-substituted orunsubstituted cycloalkyl, R^(45a)-substituted or unsubstitutedheterocycloalkyl, R^(45a)-substituted or unsubstituted aryl, orR^(45a)-substituted or unsubstituted heteroaryl.

R^(45a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(46a)-substituted or unsubstituted alkyl,R^(46a)-substituted or unsubstituted heteroalkyl, R^(46a)-substituted orunsubstituted cycloalkyl, R^(46a)-substituted or unsubstitutedheterocycloalkyl, R^(46a)-substituted or unsubstituted aryl, orR^(46a)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(10a) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(47a)-substituted or unsubstituted alkyl, R^(47a)-substituted orunsubstituted heteroalkyl, R^(47a)-substituted or unsubstitutedcycloalkyl, R^(47a)-substituted or unsubstituted heterocycloalkyl,R^(47a)-substituted or unsubstituted aryl, or R^(47a)-substituted orunsubstituted heteroaryl.

R^(47a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(48a)-substituted or unsubstituted alkyl,R^(48a)-substituted or unsubstituted heteroalkyl, R^(48a)-substituted orunsubstituted cycloalkyl, R^(48a)-substituted or unsubstitutedheterocycloalkyl, R^(48a)-substituted or unsubstituted aryl, orR^(48a)-substituted or unsubstituted heteroaryl.

R^(48a) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(49a)-substituted or unsubstituted alkyl,R^(49a)-substituted or unsubstituted heteroalkyl, R^(49a)-substituted orunsubstituted cycloalkyl, R^(49a)-substituted or unsubstitutedheterocycloalkyl, R^(49a)-substituted or unsubstituted aryl, orR^(49a)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(7c) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(38c)-substituted or unsubstituted alkyl, R³⁸-substituted orunsubstituted heteroalkyl, R³⁸-substituted or unsubstituted cycloalkyl,R³⁸-substituted or unsubstituted heterocycloalkyl, R³⁸-substituted orunsubstituted aryl, or R³⁸-substituted or unsubstituted heteroaryl.

R^(38c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(39c)-substituted or unsubstituted alkyl,R^(39c)-substituted or unsubstituted heteroalkyl, R^(39c)-substituted orunsubstituted cycloalkyl, R^(39c)-substituted or unsubstitutedheterocycloalkyl, R^(39c)-substituted or unsubstituted aryl, orR^(39c)-substituted or unsubstituted heteroaryl.

R^(39c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(40c)-substituted or unsubstituted alkyl,R^(40c)-substituted or unsubstituted heteroalkyl, R^(40c)-substituted orunsubstituted cycloalkyl, R^(40c)-substituted or unsubstitutedheterocycloalkyl, R^(40c)-substituted or unsubstituted aryl, orR^(40c)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(8c) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(41c)-substituted or unsubstituted alkyl, R^(41c)-substituted orunsubstituted heteroalkyl, R^(41c)-substituted or unsubstitutedcycloalkyl, R^(41c)-substituted or unsubstituted heterocycloalkyl,R^(41c)-substituted or unsubstituted aryl, or R^(41c)-substituted orunsubstituted heteroaryl.

R^(41c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(42c)-substituted or unsubstituted alkyl,R^(42c)-substituted or unsubstituted heteroalkyl, R^(42c)-substituted orunsubstituted cycloalkyl, R^(42c)-substituted or unsubstitutedheterocycloalkyl, R^(42c)-substituted or unsubstituted aryl, orR^(42c)-substituted or unsubstituted heteroaryl.

R^(42c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(43c)-substituted or unsubstituted alkyl,R^(43c)-substituted or unsubstituted heteroalkyl, R^(43c)-substituted orunsubstituted cycloalkyl, R^(43c)-substituted or unsubstitutedheterocycloalkyl, R^(43c)-substituted or unsubstituted aryl, orR^(43c)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(9c) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(44c)-substituted or unsubstituted alkyl, R^(44c)-substituted orunsubstituted heteroalkyl, R^(44c)-substituted or unsubstitutedcycloalkyl, R^(44c)-substituted or unsubstituted heterocycloalkyl,R^(44c)-substituted or unsubstituted aryl, or R^(44c)-substituted orunsubstituted heteroaryl.

R^(44c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(45c)-substituted or unsubstituted alkyl,R^(45c)-substituted or unsubstituted heteroalkyl, R^(45c)-substituted orunsubstituted cycloalkyl, R^(45c)-substituted or unsubstitutedheterocycloalkyl, R^(45c)-substituted or unsubstituted aryl, orR^(45c)-substituted or unsubstituted heteroaryl.

R^(45c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(46c)-substituted or unsubstituted alkyl,R^(46c)-substituted or unsubstituted heteroalkyl, R^(46c)-substituted orunsubstituted cycloalkyl, R^(46c)-substituted or unsubstitutedheterocycloalkyl, R^(46c)-substituted or unsubstituted aryl, orR^(46c)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R^(10c) isindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,R^(47c)-substituted or unsubstituted alkyl, R^(47c)-substituted orunsubstituted heteroalkyl, R^(47c)-substituted or unsubstitutedcycloalkyl, R^(47c)-substituted or unsubstituted heterocycloalkyl,R^(47c)-substituted or unsubstituted aryl, or R^(47c)-substituted orunsubstituted heteroaryl.

R^(47c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(48c)-substituted or unsubstituted alkyl,R^(48c)-substituted or unsubstituted heteroalkyl, R^(48c)-substituted orunsubstituted cycloalkyl, R^(48c)-substituted or unsubstitutedheterocycloalkyl, R^(48c)-substituted or unsubstituted aryl, orR^(48c)-substituted or unsubstituted heteroaryl.

R^(48c) is independently oxo, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, R^(49c)-substituted or unsubstituted alkyl,R^(49c)-substituted or unsubstituted heteroalkyl, R^(49c)-substituted orunsubstituted cycloalkyl, R^(49c)-substituted or unsubstitutedheterocycloalkyl, R^(49c)-substituted or unsubstituted aryl, orR^(49c)-substituted or unsubstituted heteroaryl.

In some embodiments of the compounds provided herein, R²², R²⁵, R^(25A),R^(25B), R^(25C), R²⁸, R³¹, R³⁴, R³⁷, R⁴⁰, R⁴³, R⁴⁶, R⁴⁹, R⁵⁸, R⁶¹, R⁶⁴,R⁶⁷, R⁷⁰, R^(40a), R^(43a), R^(46a), R^(49a), R^(40c), R^(43c), R^(46c),R^(49c), are independently hydrogen, oxo, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, unsubstituted alkyl, unsubstituted heteroalkyl,unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstitutedaryl, or unsubstituted heteroaryl.

In some embodiments, the compound has the Formula:

R³, e5, R^(2A). R^(2B), L², L³, and E are as described herein and above(including embodiments). X′ is —O—, —NH—, or —S—. E is an electrophilicchemical moiety capable of forming a covalent bond with a cysteine oraspartate residue; R^(2C) is independently hydrogen, oxo, halogen,—CX^(c) ₃, —CN, —SO₂Cl, —SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c), —NHNH₂,—ONR^(7c)R^(8c), —NHC═(O)NHNH₂, —NHC═(O)NR^(7c)R^(8c), —N(O)_(m3),—NR^(7c)R^(8c), —C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c),—OR^(10c), —NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c),—NR^(7c)C(O)—OR^(9c), —NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; two adjacent R^(2C)substituents may optionally be joined to form a substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; two R^(2C) substituents bonded to the same atom mayoptionally be joined to form a substituted or unsubstituted cycloalkylor substituted or unsubstituted heterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰are independently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH,—CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R^(7a),R^(8a), R^(9a) and R^(10a) are independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl;R^(7a) and R^(8a) substituents bonded to the same nitrogen atom mayoptionally be joined to form a substituted or unsubstitutedheterocycloalkyl or substituted or unsubstituted heteroaryl; R^(7c),R^(8c), R^(9c) and R^(10c) are independently hydrogen, halogen, —CF₃,—CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂,—NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H,—NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted or unsubstituted alkyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heterocycloalkyl, substitutedor unsubstituted aryl, or substituted or unsubstituted heteroaryl; m,m1, m3, v, v1, and v3 are independently 1 or 2; n, n1, and n3 areindependently an integer from 0 to 4; X, X^(a) and X^(c) areindependently —Cl, —Br, —I, or —F.

In some embodiments, E comprises a substituted or unsubstituted vinylsulfone moiety, substituted or unsubstituted vinyl sulfonamide moiety,substituted or unsubstituted peroxide moiety, substituted orunsubstituted fluoro(C₁-C₄)alkylketone moiety, substituted orunsubstituted chloro(C₁-C₄)alkylketone moiety, substituted orunsubstituted acrylamide moiety, substituted or unsubstituted disulfidemoiety, substituted or unsubstituted thiol moiety, substituted orunsubstituted phosphonate moiety, substituted or unsubstituted aldehydemoiety, substituted or unsubstituted enone moiety, substituted orunsubstituted diazomethylketone moiety, substituted or unsubstituteddiazomethylamide moiety, substituted or unsubstituted cyanocyclopropylcarboxamide moiety, substituted or unsubstituted epoxide moiety,substituted or unsubstituted epoxyketone moiety, substituted orunsubstituted epoxyamide moiety, substituted or unsubstituted arylaldehyde moiety, substituted or unsubstituted aryl dialdehyde moiety,substituted or unsubstituted dialdehyde moiety, substituted orunsubstituted nitrogen mustard moiety, substituted or unsubstitutedpropargyl moiety, substituted or unsubstituted propargylamide moiety. Insome embodiments, E is a substituted or unsubstituted vinyl sulfonemoiety, substituted or unsubstituted vinyl sulfonamide moiety,substituted or unsubstituted peroxide moiety, substituted orunsubstituted fluoro(C₁-C₄)alkylketone moiety, substituted orunsubstituted chloro(C₁-C₄)alkylketone moiety, substituted orunsubstituted acrylamide moiety, substituted or unsubstituted disulfidemoiety, substituted or unsubstituted thiol moiety, substituted orunsubstituted phosphonate moiety, substituted or unsubstituted aldehydemoiety, substituted or unsubstituted enone moiety, substituted orunsubstituted diazomethylketone moiety, substituted or unsubstituteddiazomethylamide moiety, substituted or unsubstituted cyanocyclopropylcarboxamide moiety, substituted or unsubstituted epoxide moiety,substituted or unsubstituted epoxyketone moiety, substituted orunsubstituted epoxyamide moiety, substituted or unsubstituted arylaldehyde moiety, substituted or unsubstituted aryl dialdehyde moiety,substituted or unsubstituted dialdehyde moiety, substituted orunsubstituted nitrogen mustard moiety, substituted or unsubstitutedpropargyl moiety, substituted or unsubstituted propargylamide moiety.

In some embodiments, L² is independently R^(2C)-substituted orunsubstituted heterocycloalkylene or R^(2C)-substituted or unsubstitutedspirocyclic linker and L³ is a bond. For example, L² is monocyclic 4, 5,or 6-membered heterocycloalkylene. In some embodiments, L² isunsubstituted piperazino or unsubstituted piperidino. In otherembodiments, L² is bicyclic fused heterocycloalkylene. In yet otherembodiments, L² is an unsubstituted spirocyclic linker.

In some embodiments of the above compounds, E comprises a substituted orunsubstituted vinyl sulfone moiety, substituted or unsubstituted vinylsulfonamide moiety, or a substituted or unsubstituted acrylamide moiety.In some embodiments of the above compounds, E is a substituted orunsubstituted vinyl sulfone moiety, substituted or unsubstituted vinylsulfonamide moiety, or a substituted or unsubstituted acrylamide moiety.

In some embodiments, the compound has the Formula:

In some embodiments, the compound binds Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) behindSwitch II. In embodiments, the compound modulates the conformation ofSwitch II. In embodiments, the compound modulates the conformation ofSwitch I. In embodiments, the compound modulates the conformation ofSwitch I and Switch II. In embodiments, the compound inhibits (e.g. byabout 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, 3.0, 4.0,5.0, 6.0, 7.0, 8.0, 9.0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25,30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300,400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000,8000, 9000, 10000 fold or more) Ras (e.g. K-Ras, H-Ras, N-Ras, mutantRas, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) nucleotide exchange(e.g. GDP for GTP or GTP for GDP) relative to the absence of thecompound. In embodiments, the compound inhibits release of GDP from Ras(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) relative to the absence of the compound. Inembodiments, the compound inhibits binding of GDP to Ras (e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) relative to the absence of the compound. In embodiments, thecompound inhibits binding of GTP to Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative tothe absence of the compound. In embodiments, the compound increases(e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0,3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100,200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000,6000, 7000, 8000, 9000, 10000 fold or more) Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)nucleotide exchange (e.g. GDP for GTP or GTP for GDP) relative to theabsence of the compound. In embodiments, the compound increases releaseof GDP from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) relative to the absence of the compound.In embodiments, the compound increases release of GTP from Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) relative to the absence of the compound. In embodiments, thecompound increases binding of GDP to Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative tothe absence of the compound. In embodiments, the compound inhibitsbinding of GTP to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the absence of thecompound. In embodiments, the compound inhibits binding of a GTP analog(e.g. mant-dGTP) to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the absence of thecompound. In embodiments, the compound modulates the conformation of aRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) amino acid that contacts GTP in the absence of thecompound. In embodiments, the compound modulates the conformation of aRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) amino acid that contacts GDP in the absence of thecompound. In embodiments, the compound modulates the conformation of aplurality of Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acids that contact GTP in theabsence of the compound. In embodiments, the compound modulates theconformation of a plurality of Ras (e.g. K-Ras, H-Ras, N-Ras, mutantRas, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acids thatcontact GDP in the absence of the compound. In embodiments, the compoundmodulates the binding of GTP and/or GDP to Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)compared to binding in the absence of the compound. In embodiments, thecompound modulates the release of GTP and/or GDP from Ras (e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) compared to release in the absence of the compound. Inembodiments, the compound modulates the ratio of the binding of GTP andGDP to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) compared to the ratio in the absence ofthe compound. In embodiments, the compound modulates the ratio of therate of release of GTP and GDP from Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) compared tothe ratio in the absence of the compound. In embodiments, the compoundmodulates the conformation of a Ras amino acid that contacts the gammaphosphate of GTP when GTP is bound to Ras. In embodiments, the compoundinhibits the binding of the gamma phosphate of GTP relative to thebinding in the absence of the compound. In embodiments, the compoundbinds Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,K-Ras G12D, K-Ras G13D) protein bound to GDP and, after release of theGDP, modulates the subsequent binding of GDP or GTP to the Ras bound tothe compound. In embodiments, the compound binds Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)protein bound to GDP and, after release of the GDP, modulates thesubsequent binding of GDP to the Ras bound to the compound. Inembodiments, the compound binds Ras (e.g. K-Ras, H-Ras, N-Ras, mutantRas, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) protein bound toGDP and after release of the GDP, modulates the subsequent binding ofGTP to the Ras bound to the compound.

In embodiments, the compound inhibits proliferation of cancer cellsunder nutrient deficient conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder nutrient deficient conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder nutrient deficient conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder serum deprivation conditions relative to the absence of thecompound. In embodiments, the compound inhibits proliferation of cancercells under serum deprivation conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder conditions (e.g. local cell environment in a patient) mimickingserum deprivation relative to the absence of the compound. Inembodiments, the compound inhibits proliferation of cancer cells underconditions (e.g. local cell environment in a patient) mimicking serumdeprivation relative to the absence of the compound.

In embodiments, the compound modulates the conformation of the aminoacid corresponding to amino acid 60 in human K-Ras in a Ras protein. Inembodiments, the compound modulates the distance between the alphacarbon of the amino acid corresponding to amino acid 12 in human K-Rasand the alpha carbon of the amino acid corresponding to amino acid 60 inhuman K-Ras, in a Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D). In embodiments thecompound increases the distance between the alpha carbon of the aminoacid corresponding to amino acid 12 in human K-Ras and the alpha carbonof the amino acid corresponding to amino acid 60 in human K-Ras, in aRas protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D). In embodiments the compound increases thedistance (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9,1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3,2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7,3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1,5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5,6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9,8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3,9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6,10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8,11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2,14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4,15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6,17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8,18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0,or more angstroms) between the alpha carbon of the amino acidcorresponding to amino acid 12 in human K-Ras and the alpha carbon ofthe amino acid corresponding to amino acid 60 in human K-Ras, in a Rasprotein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,K-Ras G12D, K-Ras G13D) relative to the absence of the compound. Inembodiments the compound increases the distance (e.g. by about 0.1, 0.2,0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6,1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0,3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4,4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2,7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6,8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0,10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2,11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4,12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6,13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8,14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0,17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2,18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4,19.5, 19.6, 19.7, 19.8, 19.9, 20.0, or more angstroms) between the alphacarbon of the amino acid corresponding to amino acid 12 in human K-Rasand the alpha carbon of the amino acid corresponding to amino acid 60 inhuman K-Ras, in a Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) when bound to GDP,relative to the absence of the compound. In embodiments the compoundincreases the distance (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1,2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5,3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9,5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3,6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1,9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4,10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6,11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8,12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0,14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4,17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6,18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8,19.9, 20.0, or more angstroms) between the alpha carbon of the aminoacid corresponding to amino acid 12 in human K-Ras and the alpha carbonof the amino acid corresponding to amino acid 60 in human K-Ras, in aRas protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) when bound to GTP, compared to thedistance in the absence of the compound. In embodiments, upon binding toRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) the compound (e.g. a compound described herein,including embodiments and including a compound described in a table,example, or figure) modulates the distance between the alpha carbon ofthe amino acid corresponding to amino acid 12 in human K-Ras and thealpha carbon of the amino acid corresponding to amino acid 60 in humanK-Ras, in the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to be about 4.9 angstroms orgreater (e.g. about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9,5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3,6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1,9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4,10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6,11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8,12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0,14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4,17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6,18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8,19.9, 20.0 angstroms, or greater). In embodiments, upon binding to Ras(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) the compound (e.g. a compound described herein,including embodiments and including a compound described in a table,example, or figure) modulates the distance between the alpha carbon ofthe amino acid corresponding to amino acid 12 in human K-Ras and thealpha carbon of the amino acid corresponding to amino acid 60 in humanK-Ras, in the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to be greater than about 4.9angstroms (e.g. greater than about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6,5.7, 5.8, 5.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0,6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4,7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8,8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2,10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4,11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6,12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8,13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0,15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2,17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4,18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6,19.7, 19.8, 19.9, 20.0 angstroms, or greater). In embodiments, uponbinding to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) the compound (e.g. a compound describedherein, including embodiments and including a compound described in atable, example, or figure) modulates the distance between the alphacarbon of the amino acid corresponding to amino acid 12 in human K-Rasand the alpha carbon of the amino acid corresponding to amino acid 60 inhuman K-Ras, in the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to be 4.9 angstroms orgreater (e.g. 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0,5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4,6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8,7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2,9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5,10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7,11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9,13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1,14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3,15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5,17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7,18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9,20.0 angstroms, or greater). In embodiments, upon binding to Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) the compound (e.g. a compound described herein, includingembodiments and including a compound described in a table, example, orfigure) modulates the distance between the alpha carbon of the aminoacid corresponding to amino acid 12 in human K-Ras and the alpha carbonof the amino acid corresponding to amino acid 60 in human K-Ras, in theRas protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) to be greater than 4.9 angstroms (e.g.greater than 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0, 5.1,5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5,6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9,8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3,9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6,10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8,11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2,14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4,15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6,17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8,18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0angstroms, or greater).

In embodiments, the compound increases the flexibility of Switch Irelative to the absence of the compound. In embodiments, the compoundincreases the disorder of Switch I relative to the absence of thecompound. In embodiments, the compound inhibits the binding of Ras((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) to another protein. In embodiments, the compoundinhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to another protein,wherein the binding is dependent on Ras binding to GTP. In embodiments,the compound inhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to anotherprotein, wherein the binding is dependent on Ras binding to GDP. Inembodiments, the compound inhibits the binding of Ras ((e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) to Raf (e.g. Raf1). In embodiments, the compound inhibits thebinding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) to SOS. In embodiments, the compoundinhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras) to aGEF. In embodiments, the compound inhibits the binding of Ras ((e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) to PI3K. In embodiments, the compound modulates metalbinding near the nucleotide binding site. In embodiments, the compoundmodulates the conformation of the Ras metal binding site near thenucleotide binding site. In embodiments, the compound modulates theconformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid relative to theconformation in the absence of the compound, wherein the Ras amino acidconformation is also modulated by a Ras G60 mutation. In embodiments,the compound modulates the conformation of a Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) aminoacid relative to the conformation in the absence of the compound,wherein the Ras amino acid conformation is also modulated by a Ras G60Amutation. In embodiments, the compound modulates the conformation of aRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) amino acid relative to the conformation in the absenceof the compound, wherein the Ras amino acid conformation is alsomodulated by a Ras T35 mutation. In embodiments, the compound modulatesthe conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid relative to theconformation in the absence of the compound, wherein the Ras amino acidconformation is also modulated by a Ras T35S mutation. In embodiments,the compound modulates the conformation of a Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) aminoacid relative to the conformation in the absence of the compound,wherein the Ras amino acid conformation is also modulated by a mutationof the Ras amino acid corresponding to K-Ras G60. In embodiments, thecompound modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acidrelative to the conformation in the absence of the compound, wherein theRas amino acid conformation is also modulated by a mutation of the Rasamino acid corresponding to K-Ras T35.

The crystal structures of Hras and Kras bound to GTP show a contactbetween the gamma phosphate and the backbone amide of glycine-60 inswitch II. This contact is known to be critical for orienting theswitches for binding to downstream effectors. This conformation requiredfor binding downstream effectors is called state 2. Mutation ofglycine-60 to alanine (G60A) prevents proper rotation of residue-60 uponGTP binding, and induces an alternate conformation called state 1. Inthis conformation, the gamma phosphate of GTP forms a water-mediatedhydrogen bond to alanine-60, which likely acts to maintain GTP affinity.Similarly, direct contacts between the gamma phosphate and switch I arereplaced by water-mediated contacts. The complete loss of these contactsto the gamma phosphate would be likely to decrease the affinity of Rasfor GTP, having less effect on the affinity for GDP.

The state 1 conformation can also be stabilized by mutating threonine-35to serine (T35S), and the GTP-bound crystal structure of this mutant isknown. A crystal structure of the wild-type protein in state 1 has alsobeen solved. We noticed that the conformation of Ras (state 1 or state2) could be predicted by measuring the distance between the alpha carbonof residue-60 and the alpha carbon of residue-12. If this distance is3.9 Å or less, direct contacts between the gamma phosphate and theswitches are possible and the protein adopts state 2. If this distanceis 4.9 Å or greater, these direct contacts are no longer possible andthe protein adopts state 1.

When bound to GDP, the conformation of the protein is unaffected by theG60A mutation or the T35S mutation. In both cases, as with thewild-type, the distance between position 12 and position 60 isapproximately 8 Å. In crystal structures we have solved with ourinhibitors (e.g. a compound selected from the compounds describedherein) bound to KrasG12C, the structures show distances betweenresidue-12 and residue-60 of more than 8 Å in the GDP-bound state.Unlike the wild-type, G60A and T35S, when our inhibitor (e.g. a compoundselected from the compounds described herein) is bound this distancecannot decrease to below 5 Å upon GTP-binding due to a steric clash thatwould occur between our inhibitor and switch II. Therefore, ourinhibitors (e.g. a compound selected from the compounds describedherein) will prevent switch II from forming contacts with the gammaphosphate and, when they increase the distance between these tworesidues enough (>11 Å), even cause disordering of switch I.

Based on these observations, our compounds (e.g. a compound selectedfrom the compounds described herein) are likely to have a deleteriouseffect on GTP binding. Due to the critical contacts from the gammaphosphate to switch II, some of our compounds (e.g. a compound selectedfrom the compounds described herein) will have a greater effect on GTPbinding than on GDP binding.

In some embodiments, the compound is any one of the compounds in Table1, 2, 3, 4, or 5.

In some embodiments, a compound as described herein may include multipleinstances of R³, R⁷, R⁸, R⁹, R¹⁰, R^(2A), R^(7a), R^(8a), R^(9a),R^(10a), R^(2B), R^(2C), R^(7c), R^(8c), R^(9c), R^(10c), X, X^(a),X^(c), m, n, v, m1, n1, v1, m3, n3, v3, and/or other variables. In suchembodiments, each variable may optional be different and beappropriately labeled to distinguish each group for greater clarity. Forexample, where each R³, R⁷, R⁸, R⁹, R¹, R^(2a), R^(7a), R^(8a), R^(9a),R^(10a), R^(2B), R^(2C), R^(7c), R^(8c), R^(9c), R^(10c), X, X^(a),X^(c), m, n, v, m1, n1, v1, m3, n3, and/or v3, is different, they may bereferred to, for example, as R^(3.1), R^(3.2), R^(3.3), R^(3.4),R^(3.5), R^(3.6), R^(3.7), R^(7.1), R^(7.2), R^(7.3), R^(7.4), R^(7.5),R^(7.6), R^(7.7), R^(8.1), R^(8.2), R^(8.3), R^(8.4), R^(8.5), R^(8.6),R^(8.7), R^(9.1), R^(9.2), R^(9.3), R^(9.4), R^(9.5), R^(9.6), R^(9.7),R^(10.1), R^(10.2), R^(10.3), R^(10.4), R^(10.5), R^(10.6), R^(10.7),R^(2A.1), R^(2A.2), R^(2A.3), R^(7a.1), R^(7a.2), R^(7a.3), R^(7a.4),R^(7a.5), R^(7a.6), R^(8a.1), R^(8a.2), R^(8a.3), R^(8a.4), R^(8a.5),R^(8a.6), R^(9a.1), R^(9a2), R^(9a.3), R^(9a.4), R^(9a.5), R^(9a.6),R^(10a.1), R^(10a.2), R^(10a.3), R^(10a.4), R^(10a.5), R^(10a.6),R^(2B.1), R^(2B.2), R^(2B.3), R^(2C.1), R^(2C.2), R^(2C.3), R^(2C.4),R^(2C.5), R^(2C.6), R^(2C.7), R^(2C.8), R^(2C.9), R^(2C.10), R^(2C.11),R^(2C.12), R^(2C.13), R^(2C.14), R^(2C.15), R^(2C.16), R^(2C.17),R^(2C.18), R^(2C.19), R^(2C.20), R^(2C.21), R^(2C.22), R^(2C.23),R^(2C.24), R^(2C.25), R^(2C.26), R^(2C.27), R^(2C.28), R^(2C.29),R^(2C.30), R^(2C.31), R^(2C.32), R^(2C.33), R^(2C.34), R^(2C.35),R^(2C.36), R^(2C.37), R^(2C.38), R^(2C.39), R^(2C.40), R^(2C.41),R^(2C.42), R^(7c.1), R^(7c.2), R^(7c.3), R^(7c.4), R^(7c.5), R^(7c.6),R^(7c.7), R^(7c.8), R^(7c.9), R^(7c.10), R^(7c.11), R^(7c.12),R^(7c.13), R^(7c.14), R^(7c.15), R^(7c.16), R^(7c.17), R^(7c.18),R^(7c.19), R^(7c.20), R^(7c.21), R^(7c.22), R^(7c.23), R^(7c.24),R^(7c.25), R^(7c.26), R^(7c.27), R^(7c.28), R^(7c.29), R^(7c.30),R^(7c.31), R^(7c.32), R^(7c.33), R^(7c.34), R^(7c.35), R^(7c.36),R^(7c.37), R^(7c.38), R^(7c.39), R^(7c.40), R^(7c.41), R^(7c.42),R^(8c.1), R^(8c.2), R^(8c.3), R^(8c.4), R^(8c.5), R^(8c.6), R^(8c.7),R^(8c.8), R^(8c.9), R^(8c.10), R^(8c.11), R^(8c.12), R^(8c.13),R^(8c.14), R^(8c.15), R^(8c.16), R^(8c.17), R^(8c.18), R^(8c.19),R^(8c.20), R^(8c.21), R^(8c.22), R^(8c.23), R^(8c.24), R^(8c.25),R^(8c.26), R^(8c.27), R^(8c.28), R^(8c.29), R^(8c.30), R^(8c.31),R^(8c.32), R^(8c.33), R^(8c.34), R^(8c.35), R^(8c.36), R^(8c.37),R^(8c.38), R^(8c.39), R^(8c.40), R^(8c.41), R^(8c.42), R^(9c.1),R^(9c.2), R^(9c.3), R^(9c.4), R^(9c.5), R^(9c.6), R^(9c.7), R^(9c.8),R^(9c.9), R^(9c.10), R^(9c.11), R^(9c.12), R^(9c.13), R^(9c.14),R^(9c.15), R^(9c.16), R^(9c.17), R^(9c.18), R^(9c.19), R^(9c.20),R^(9c.21), R^(9c.22), R^(9c.23), R^(9c.24), R^(9c.25), R^(9c.26),R^(9c.27), R^(9c.28), R^(9c.29), R^(9c.30), R^(9c.31), R^(9c.32),R^(9c.33), R^(9c.34), R^(9c.35), R^(9c.36), R^(9c.37), R^(9c.38),R^(9c.39), R^(9c.40), R^(9c.41), R^(9c.42), R^(10c.1), R^(10c.2),R^(10c.3), R^(10c.4), R^(10c.5), R^(10c.6), R^(10c.7), R^(10c.8),R^(10c.9), R^(10c.10), R^(10c.11), R^(10c.12), R^(10c.13), R^(10c.14),R^(10c.15), R^(10c.16), R^(10c.17), R^(10c.18), R^(10c.19), R^(10c.20),R^(10c.21), R^(10c.22), R^(10c.23), R^(10c.24), R^(10c.25), R^(10c.26),R^(10c.27), R^(10c.28), R^(10c.29), R^(10c.30), R^(10c.31), R^(10c.32),R^(10c.33), R^(10c.34), R^(10c.35), R^(10c.36), R^(10c.37), R^(10c.38),R^(10c.39), R^(10c.40), R^(10c.41), R^(10c.42), X¹, X², X³, X⁴, X⁵, X⁶,X⁷, X^(a1), X^(a2), X^(a3), X^(a4), X^(a5), X^(a6), X^(c1), X^(c2),X^(c3), X^(c4), X^(c5), X^(c6), X^(c7), X^(c8), X^(c9), X^(c10),X^(c11), X^(c13), X^(c14), X^(c15), X^(c16), X^(c17), X^(c18), X^(c19),X^(c20), X^(c21), X^(c22), X^(c23), X^(c24), X^(c25), X^(c26), X^(c27),X^(c28), X^(c29), X^(c30), X^(c31), X^(c32), X^(c33), X^(c34), X^(c35),X^(c36), X^(c37), X^(c38), X^(c39), X^(c40), X^(c41), X^(c42), m¹, m²,m³, m⁴, m⁵, m⁶, m⁷, n¹, n², n³, n⁴, n⁵, n⁶, n⁷, v¹, v², v², v³, v⁴, v⁵,v⁶, v⁷, m1¹, m1², m1³, m1⁴, m1⁵, m1⁶, n1¹, n1², n1³, n1⁴, n1⁵, n1⁶, v1¹,v1², v1³, v1⁴ v1⁵ v1⁶, m3¹, m3², m3³, m3⁴, m3⁵, m3⁶, m3⁷, m3⁸, m3⁹,m3¹⁰, m3¹¹, m3¹², m3¹³, m3¹⁴, m3¹⁵, m3¹⁶, m3¹⁷, m3¹⁸, m3¹⁹, m3²⁰, m3²¹,m3²², m3²³, m3²⁴, m3²⁵, m3²⁶, m3²⁷, m3²⁸, m3²⁹, m3³⁰, m3³¹, m3³², m3³³,m3³⁴, m3³⁵, m3³⁶, m3³⁷, m3³⁸, m3³⁹, m3⁴⁰, m3⁴¹, m3⁴², n3¹, n3², n3³,n3⁴, n3⁵, n3⁶, n3⁷, n3⁸, n3⁹, n3¹⁰, n3¹¹, n3¹², n3¹³, n3¹⁴, n3¹⁵, n3¹⁶,n3¹⁷, n3¹⁸, n3¹⁹, n3²⁰, n3²¹, n3²², n3²³, n3²⁴, n3²⁵, n3²⁶, n3²⁷, n3²⁸,n3²⁹, n3³⁰, n3³¹, n3³², n3³³, n3³⁴, n3³⁵, n3³⁶, n3³⁷, n3³⁸, n3³⁹, n3⁴⁰,n3⁴¹, n3⁴², v3¹, v3², v3³, v3⁴, v3⁵, v3⁶, v3⁷, v3⁸, v3⁹, v3¹⁰, v3¹¹,v3¹², v3¹³, v3¹⁴, v3¹⁵, v3¹⁶, v3¹⁷, v3¹⁸, v3¹⁹, v3²⁰, v3²¹, v3²², v3²³,v3²⁴, v3²⁵, v3²⁶, v3²⁷, v3²⁸, v3²⁹, v3³⁰, v3³¹, v3³², v3³³, v3³⁴, v3³⁵,v3³⁶, v3³⁷, v3³⁸, v3³⁹, v3⁴⁰, v3⁴¹, v3⁴², respectively, wherein thedefinition of R³ is assumed by R^(3.1), R^(3.2), R^(3.3), R^(3.4),R^(3.5), R^(3.6), R^(3.7), the definition of R⁷ is assumed by R^(7.1),R^(7.2), R^(7.3), R^(7.4), R^(7.5), R^(7.6), R^(7.7), the definition ofR⁸ is assumed by R^(8.1), R^(8.2), R^(8.3), R^(8.4), R^(8.5), R^(8.6),R^(8.7), the definition of R⁹ is assumed by R^(9.1), R^(9.2), R^(9.3),R^(9.4), R^(9.5), R^(9.6), R^(9.7), the definition of R¹⁰ is assumed byR^(10.1), R^(10.2), R^(10.3), R^(10.4), R^(10.5), R^(10.6), R^(10.7),the definition of R^(2A) is assumed by R^(2A.1), R^(2A.2), R^(2A.3), thedefinition of R^(7a) is assumed by R^(7a.1), R^(7a.2), R^(7a.3),R^(7a.4), R^(7a.5), R^(7a.6), the definition of R^(8a) is assumed bylead, R^(8a.2), R^(8a.3), R^(8a.4), R^(8a.5), R^(8a.6), the definitionof R^(9a) is assumed by R^(9a.1), R^(9a.2), R^(9a.3), R^(9a.4),R^(9a.5)R^(9a.6), the definition of R^(10a) is assumed by R^(10a.1),R^(10a.2), R^(10a.3), R^(10a.4), R^(10a.5), R^(10a.6), R^(2B.2), thedefinition of R^(2B.1) is assumed by R^(2B.2), R^(2B.3), the definitionof R^(2C) is assumed by R^(2C.1), R^(2C.2), R^(2C.3), R^(2C.4),R^(2C.5), R^(2C.6), R^(2C.7), R^(2C.8), R^(2C.9), R^(2C.10), R^(2C.11),R^(2C.12), R^(2C.13), R^(2C.14), R^(2C.15), R^(2C.16), R^(2C.17),R^(2C.18), R^(2C.19), R^(2C.20), R^(2C.21), R^(2C.22), R^(2C.23),R^(2C.24), R^(2C.25), R^(2C.26), R^(2C.27), R^(2C.28), R^(2C.29),R^(2C.30), R^(2C.31), R^(2C.32), R^(2C.33), R^(2C.34), R^(2C.35),R^(2C.36), R^(2C.37), R^(2C.38), R^(2C.39), R^(2C.40), R^(2C.41),R^(2C.42), the definition of R^(7c) is assumed by R^(7c-1), R^(7c.2),R^(7c.3), R^(7c.4), R^(7c.5), R^(7c.6), R^(7c.7), R^(7c.8), R^(7c.9),R^(7c.10), R^(7c.11), R^(7c.12), R^(7c.13), R^(7c.14), R^(7c.15),R^(7c.16), R^(7c.17), R^(7c.18), R^(7c.19), R^(7c.20), R^(7c.21),R^(7c.22), R^(7c.23), R^(7c.24), R^(7c.25), R^(7c.26), R^(7c.27),R^(7c.28), R^(7c.29), R^(7c.30), R^(7c.31), R^(7c.32), R^(7c.33),R^(7c.34), R^(7c.35), R^(7.36), R^(7.37), R^(7.38), R^(7.39), R^(7.40),R^(7.41), R^(7.42), the definition of R^(8c) is assumed by R^(8.1),R^(8.2), R^(8.3), R^(8.4), R^(8.5), R^(8.6), R^(8.7), R^(8.8), R^(8.9),R^(8.10), R^(8.11), R^(8.12), R^(8.13), R^(8.14), R^(8.15), R^(8.16),R^(8.17), R^(8.18), R^(8.19), R^(8.20), R^(8.21), R^(8.22), R^(8.23),R^(8.24), R^(8.25), R^(8.26), R^(8.27), R^(8.28), R^(8.29), R^(8.30),R^(8.31), R^(8.32), R^(8.33), R^(8.34), R^(8.35), R^(8.36), R^(8.37),R^(8.38), R^(8.39), R^(8.40), R^(8.41), R^(8.42), the definition ofR^(9c) is assumed by R^(9c.1), R^(9c. 2), R^(9c.3), R^(9c.4), R^(9c.5),R^(9c.6), R^(9c.7), R^(9c.8), R^(9c.9), R^(9c.10), R^(9c.11), R^(9c.12),R^(9c.13), R^(9c.14), R^(9c.15), R^(9c.16), R^(9c.17), R^(9c.18),R^(9c.19), R^(9c.20), R^(9c.21), R^(9c.22), R^(9c.23), R^(9c.24),R^(9c.25), R^(9c.26), R^(9c.27), R^(9c.28), R^(9c.29), R^(9c.30),R^(9c.31), R^(9c.32), R^(9c.33), R^(9c.34), R^(9c.35), R^(9c.36),R^(9c.37), R^(9c.38), R^(9c.39), R^(9c.40), R^(9c.41), R^(9c.42), thedefinition of R^(10c) is assumed by R^(10c.1), R^(10c.2), R^(10c.3),R^(10c.4), R^(10c.5), R^(10c.6), R^(10c.7), R^(10c.8), R^(10c.9),R^(10c.10), R^(10c.11), R^(10c.12), R^(10c.13), R^(10c.14), R^(10c.15),R^(10c.16), R^(10c.17), R^(10c.18), R^(10c.19), R^(10c.20), R^(10c.21),R^(10c.22), R^(10c.23), R^(10c.24), R^(10c.25), R^(10c.26), R^(10c.27),R^(10c.28), R^(10c.29), R^(10c.30), R^(10c.31), R^(10c.32), R^(10c.33),R^(10c.34), R^(10c.35), R^(10c.36), R^(10c.37), R^(10c.38), R^(10c.39),R^(10c.40), R^(10c.41), R^(10c.42), the definition of X is assumed byX¹, X², X³, X⁴, X⁵, X⁶, X⁷, the definition of X^(a) is assumed byX^(a1), X^(a2), X^(a3), X^(a4), X^(a5), X^(a6), the definition of X^(c)is assumed by X^(c1), X^(c2), X^(c3), X^(c4), X^(c5), X^(c6), X^(c7),X^(c8), X^(c9), X^(c10), X^(c11), X^(c12), X^(c13), X^(c14), X^(c15),X^(c16), X^(c17), X^(c18), X^(c19), X^(c20), X^(c21), X^(c22), X^(c23),X^(c24), X^(c25), X^(c26), X^(c27), X^(c28), X^(c29), X^(c30), X^(c31),X^(c32), X^(c33), X^(c34), X^(c35), X^(c36), X^(c37), X^(c38), X^(c39),X^(c40), X^(c41), X^(c42), the definition of m is assumed by m¹, m², m³,m⁴, m⁵, m⁶, m⁷, the definition of n is assumed by n¹, n², n³, n⁴, n⁵,n⁶, n⁷, the definition of v is assumed by v¹, v², v³, v⁴, v⁵, v⁶, v⁷,the definition of m¹ is assumed by m1¹, m1², m1³, m1⁴, m1⁵, m1⁶, thedefinition of n¹ is assumed by n1¹, n1², n1³, n1⁴, n1⁵, n1⁶, thedefinition of v1 is assumed by v1¹, v1², v1³, v1⁴, v1⁵, v1⁶, thedefinition of m3 is assumed by m3¹, m3², m3³, m3⁴, m3⁵, m3⁶, m3⁷, m3⁸,m3⁹, m3¹⁰, m3¹¹, m3¹², m3¹³, m3¹⁴, m3¹⁵, m3¹⁶, m3¹⁷, m3¹⁸, m3¹⁹, m3²⁰,m3²¹, m3²², m3²³, m3²⁴, m3²⁵, m3²⁶, m3²⁷, m3²⁸, m3²⁹, m3³⁰, m3³¹, m3³²,m3³³, m3³⁴, m3³⁵, m3³⁶, m3³⁷, m3³⁸, m3³⁹, m3⁴⁰, m3⁴¹, m3⁴², thedefinition of n³ is assumed by n3¹, n3², n3³, n3⁴, n3⁵, n3⁶, n3⁷, n3⁸,n3⁹, n3¹⁰, n3¹¹, n3¹², n3¹³, n3¹⁴, n3¹⁵, n3¹⁶, n3¹⁷, n3¹⁸, n3¹⁹, n3²⁰,n3²¹, n3²², n3²³, n3²⁴, n3²⁵, n3²⁶, n3²⁷, n3²⁸, n3²⁹, n3³⁰, n3³¹, n3³²,n3³³, n3³⁴, n3³⁵, n3³⁶, n3³⁷, n3³⁸, n3³⁹, n3⁴⁰, n3⁴¹, n3⁴², thedefinition of v3 is assumed by v3¹, v3², v3³, v3⁴, v3⁵, v3⁶, v3⁷, v3⁸,y3⁹, y3¹⁰, y3¹¹, v3¹², v3¹³, v3¹⁴, v3¹⁵, v3¹⁶, v3¹⁷, v3¹⁸, v3¹⁹, v3²⁰,v3²¹, v3²², v3²³, v3²⁴, v3²⁵, v3²⁶, v3²⁷, v3²⁸, v3²⁹, v3³⁰, v3³¹, v3³²,v3³³, v3³⁴, v3³⁵, v3³⁶, v3³⁷, v3³⁸, v3³⁹, v3⁴⁰, v3⁴¹, v3⁴².

The variables used within a definition of R³, R⁷, R⁸, R⁹, R¹⁰, R^(2A),R^(7a), R^(8a), R^(9a), R^(10a), R^(2B), R^(2C), R^(7c), R^(8c), R^(9c),R^(10c), X, X^(a), X^(c), m, n, v, m1, n1, v1, m3, n3, v3, and/or othervariables that appear at multiple instances and are different maysimilarly be appropriately labeled to distinguish each group for greaterclarity.

Pharmaceutical Compositions and Methods

In a second aspect, a pharmaceutical composition including apharmaceutically acceptable excipient and a compound described herein(including embodiments, examples, and any compound in Table 1, 2, 3, 4,or 5) is provided.

In a third aspect, a method of treating a disease in a patient in needof such treatment is provided. The method including administering atherapeutically effective amount of a compound described herein(including embodiments, examples, and any compound in Table 1, 2, 3, 4,or 5) to the patient. In some embodiments, the disease is cancer. Insome embodiments, the cancer is lung cancer, colorectal cancer, coloncancer, pancreatic cancer, breast cancer, or leukemia. In someembodiments, the cancer is lung cancer. In some embodiments, the canceris non-small cell lung cancer. In some embodiments, the cancer is coloncancer. In some embodiments, the cancer is colorectal cancer. In someembodiments, the cancer is breast cancer. In some embodiments, thecancer is leukemia. In some embodiments, the cancer is pancreaticcancer. In some embodiments, the cancer is a cancer associated withaberrant K-Ras. In some embodiments, the cancer is a cancer associatedwith a mutant K-Ras. In some embodiments, the cancer is a cancerassociated with K-Ras G12C. In some embodiments, the cancer is a cancerassociated with K-Ras G12D. In some embodiments, the cancer is a cancerassociated with K-Ras G13C. In some embodiments, the cancer is a cancerassociated with K-Ras G13D.

In some embodiments, a method of treating a disorder in a subject inneed thereof is provided, comprising a) determining the presence orabsence of a mutation in a Ras protein (such as in a K-Ras, N-Ras, orH-Ras protein) in a malignant or neoplastic cell isolated from thesubject and b) if the mutation is determined to be present in thesubject, administering to the subject a therapeutically effective amountof a compound or pharmaceutically acceptable salt of the invention. Insome embodiments, the disorder is cancer.

Various methods are suitable for determining the presence of absence ofa mutation in a Ras protein in a cell isolated from a subject. As usedherein, the term “mutation” is used to refer to deletions, insertionsand/or substitutions as indicated. For example, assays can be performedto determine the presence of a nucleic acid sequence in the cell, wherethe nucleic acid sequence or a fragment thereof encodes the Ras protein.In some embodiments, nucleic acid detection comprises the use of ahybridization assay. Generally, a hybridization assay involveshybridization between complimentary sequences of one or more pairs ofpolynucleotides, such as between an oligonucleotide and an extracted oramplified genomic DNA. Non-limiting examples of hybridization assays forgenotyping SNPs include polymerase chain reaction (PCR) assays, blottingassays, TaqMan assays (Life Technologies; Carlsbad, Calif.), massspectroscopy assays, sequencing assays, gel electrophoresis, ELISA,MALDI-TOF mass spectrometry hybridization, primer extension,fluorescence detection, fluorescence resonance energy transfer (FRET),fluorescence polarization, microchannel electrophoresis, microarray,southern blot, northern blot, slot blot, dot blot, single primer linearnucleic acid amplification, as described in U.S. Pat. No. 6,251,639,SNP-IT, GeneChips (Affymetrix; Santa Clara, Calif.), HuSNP (Affymetrix;Santa Clara, Calif.), BeadArray (Illumina; San Diego, Calif.), Invaderassay (Hologic; Bedford, Mass.), MassEXTEND (Sequenom; San DiegoCalif.), MassCLEAVE (hMC) method (Sequenom; San Diego Calif.), andothers. PCR assays include any assays utilizing a PCR amplificationprocess. In some embodiments, the PCR assay comprises the use ofoligonucleotide primers that hybridize only to the variant or wild typeallele (e.g., to the region of polymorphism or mutation) of a diallelicSNP. PCR assays may also combine amplification with probe hybridization,such as in a TaqMan assay (see e.g., U.S. Pat. Nos. 5,962,233 and5,538,848, each of which is herein incorporated by reference) where theassay is performed during a PCR reaction. Alternatively, detection ofone or more mutations may utilize a SNP-IT primer extension assay(Orchid Cellmark, Burlington, N.C.; See e.g., U.S. Pat. Nos. 5,952,174and 5,919,626, each of which is herein incorporated by reference). Inother embodiments, a mass spectroscopy-based assay is used, such as aMassARRAY system (Sequenom; San Diego Calif.). See for example U.S. Pat.Nos. 6,043,031; 5,777,324; and 5,605,798, incorporated herein byreference. Detection of one or more mutations may also utilize an arrayof probes (also referred to as a “DNA chip” assay, e.g. a GeneChipassay—Affymetrix, Santa Clara, Calif.). See e.g., U.S. Pat. Nos.6,045,996; 5,925,525; and 5,858,659; each of which is hereinincorporated by reference. In still other embodiments, a DNA microchipcontaining electronically captured probes is used (see e.g. U.S. Pat.Nos. 6,017,696; 6,068,818; and 6,051,380; each incorporated herein byreference). In yet other embodiments, detection of mutations isperformed using a “bead array” (Illumina, San Diego, Calif.; See e.g.,PCT Publications WO 99/67641 and WO 00/39587; each incorporated hereinby reference). In other embodiments, a sample comprising nucleic acidobtained from a cell is sequenced to determine the presence of amutation. Any method known in the art may be used, for instance asdescribed in US 2011/0319290 and US 2009/0298075, each incorporatedherein by reference. Sequencing may involve, for example, precipitationof the nucleic acid followed by resuspension and sequencing usingMaxam-Gilbert sequencing, chain-termination sequencing, pyrosequencing,polony sequencing, or nanopore sequencing.

In some embodiments, a method of treating a disorder in a subject isprovided, comprising determining the presence or absence of a Rasmutation (e.g. K-Ras mutation) in a malignant or neoplastic cellisolated from the subject, in connection with the prescription aneffective amount of a compound or pharmaceutically acceptable salt ofthe invention, and, if the mutation is determined to be present in thesubject, an alert is provided to a third party which may be, forexample, a caregiver/care provider (e.g. a medical professional such asa physician, including an oncologist, a hospital, or clinic), caremanager, other health professional, a third-party payor, an insurancecompany or a government office. For example, the third party is acaregiver who is a physician. The alert may comprise providing a reportin any suitable form, such as in electronic or paper form. For example,providing the alert is performed with the aid of a processor, forexample using a computer system executing instructions contained incomputer-readable media. One or more steps of methods described here maybe implemented and/or executed, in hardware or software. Software may bestored, for example, in memory or in any other computer readable mediumand executed using a processor. Such processors may be associated withone or more controllers, calculation units, and/or other units of acomputer system or implanted in firmware. Computer readable media andmemory include RAM, ROM, flash memory, magnetic disks, laser disks, orother media. Software or alerts may be delivered to a computing deviceor between computing devices via any known delivery method, including,for example, a communication channel such as a telephone line, theinternet, a wireless connection, or via a transportable medium such as acomputer readable disk, flash drive etc. Computing devices include PCs,workstations, smartphones, tablets, PDAs or any other devices comprisingprocessors.

Reports can comprise output from the detection method such as thepresence and/or nature of the mutation. The alert may further compriseinformation regarding prognosis, resistance, or potential or suggestedtherapeutic options. The alert can comprise information on the likelyeffectiveness of a therapeutic option, the acceptability of atherapeutic option, or the advisability of applying the therapeuticoption to a patient having a mutation identified in the test. The alertcan include information, or a recommendation on, the administration of adrug, e.g., the administration at a preselected dosage or in apreselected treatment regimen, and/or in combination with other drugs,to the patient. In some embodiments, the subject is alerted if a subjectis designated as having a cancer in which aberrant Ras (e.g. H-Ras,N-Ras, or K-Ras) expression or activity is involved. For example, asubject is alerted if the subject is determined to have a mutatedversion of Ras, e.g. K-Ras. In one embodiment, an alert is provided ifthe subject is determined to have a G12C mutation.

In a fourth aspect, a method of modulating the activity of a K-Rasprotein is provided. The method including contacting the K-Ras proteinwith an effective amount of a compound described herein (includingembodiments, examples, and any compound in Table 1, 2, 3, 4, or 5). Insome embodiments, the activity of the K-Ras protein is it's GTPaseactivity, nucleotide exchange, differential GDP or GTP binding, effectorprotein binding, effector protein activation, guanine exchange factor(GEF) binding, GEF-facilitated nucleotide exchange, phosphate release,nucleotide release, nucleotide binding, K-Ras subcellular localization,K-Ras post-translational processing, K-Ras post-translationalmodifications, or a GTP bound K-Ras signaling pathway. In someembodiments, the activity of the K-Ras protein is its GTPase activity,nucleotide exchange, effector protein binding, effector proteinactivation, guanine exchange factor (GEF) binding, GEF-facilitatednucleotide exchange, phosphate release, nucleotide release, nucleotidebinding, or the activity of a GTP bound K-Ras signaling pathway. In someembodiments, the modulating of the activity of the K-Ras proteinincludes modulating the binding affinity of K-Ras for GDP. In someembodiments, the modulating of the activity of the K-Ras proteinincludes the binding affinity of K-Ras for GTP. In some embodiments, themodulating of the activity of the K-Ras protein includes modulating therelative binding affinity of K-Ras for GTP vs. GDP. In some embodiments,the activity of the K-Ras protein is the activity of a signaling pathwayactivated by GTP bound K-Ras. In some embodiments, the modulating isincreasing the activity of said K-Ras protein. In some embodiments, themodulating is reducing the activity of said K-Ras protein. In someembodiments, the K-Ras protein is a human K-Ras protein. In someembodiments, the human K-Ras protein contains a G12C mutation. In someembodiments, the human K-Ras protein contains a G12D mutation. In someembodiments, the human K-Ras protein contains a G13C mutation. In someembodiments, the human K-Ras protein contains a G13D mutation. In someembodiments, the K-Ras protein is a human K-Ras4A protein. In someembodiments, the K-Ras protein is a human K-Ras4B protein. In someembodiments, the K-Ras protein is a mutant K-Ras protein. In someembodiments, the K-Ras protein is an activated K-Ras protein. In someembodiments, the K-Ras protein is within a biological cell. In someembodiments, the biological cell forms part of an organism. In someembodiments of the method of modulating the activity of a K-Ras proteinincluding contacting the K-Ras protein with an effective amount of acompound described herein (including embodiments, examples, and anycompound in Table 1, 2, 3, 4, or 5), the compound is less effective atmodulating the activity of an H-Ras protein. In some embodiments of themethod, the compound modulates the activity of K-Ras at least two-foldmore than it modulates the activity of H-Ras. In some embodiments of themethod, the compound modulates the activity of K-Ras at least five-foldmore than it modulates the activity of H-Ras. In some embodiments of themethod, the compound modulates the activity of K-Ras at least ten-foldmore than it modulates the activity of H-Ras. In some embodiments of themethod, the compound modulates the activity of K-Ras at least fifty-foldmore than it modulates the activity of H-Ras. In some embodiments of themethod of modulating the activity of a K-Ras protein includingcontacting the K-Ras protein with an effective amount of a compounddescribed herein (including embodiments, examples, and any compound inTable 1, 2, 3, 4, or 5), the compound is less effective at modulatingthe activity of an N-Ras protein. In some embodiments of the method, thecompound modulates the activity of K-Ras at least two-fold more than itmodulates the activity of N-Ras. In some embodiments of the method, thecompound modulates the activity of K-Ras at least five-fold more than itmodulates the activity of N-Ras. In some embodiments of the method, thecompound modulates the activity of K-Ras at least ten-fold more than itmodulates the activity of N-Ras. In some embodiments of the method, thecompound modulates the activity of K-Ras at least fifty-fold more thanit modulates the activity of N-Ras.

In a fifth aspect, a method of modulating a K-Ras protein is provided.The method including contacting the K-Ras protein with an effectiveamount of a compound described herein (including embodiments, examples,and in Table 1, 2, 3, 4, or 5). In some embodiments, the K-Ras proteinis modulated in K-Ras subcellular localization, K-Ras post-translationalprocessing, K-Ras post-translational modifications, or a GTP bound K-Rassignaling pathway. In some embodiments, the modulating is increasing thepost-translational processing or modifications of the K-Ras protein. Insome embodiments, the modulating is reducing the post-translationalprocessing or modifications of the K-Ras protein. In some embodiments,the K-Ras protein is a human K-Ras protein. In some embodiments, thehuman K-Ras protein contains a G12C mutation. In some embodiments, thehuman K-Ras protein contains a G12D mutation. In some embodiments, thehuman K-Ras protein contains a G13C mutation. In some embodiments, thehuman K-Ras protein contains a G13D mutation. In some embodiments, theK-Ras protein is a human K-Ras4A protein. In some embodiments, the K-Rasprotein is a human K-Ras4B protein. In some embodiments, the K-Rasprotein is a mutant K-Ras protein. In some embodiments, the K-Rasprotein is an activated K-Ras protein. In some embodiments, the K-Rasprotein is within a biological cell. In some embodiments, the biologicalcell forms part of an organism.

In a sixth aspect, a K-Ras protein covalently bonded to a compound, forexample a compound asdescribed herein (including modulators, inhibitors,embodiments, examples, and any compound in Table 1, 2, 3, 4, or 5), isprovided. The compound is covalently bonded to a cysteine residue of theK-Ras protein. In some embodiments, the covalently modified K-Rasprotein has a modulated activity relative to a control, wherein theactivity is selected from GTPase activity, nucleotide exchange, effectorprotein binding, effector protein activation, guanine exchange factor(GEF) binding, GEF-facilitated nucleotide exchange, phosphate release,nucleotide release, nucleotide binding, K-Ras subcellular localization,K-Ras post-translational processing, and K-Ras post-translationalmodifications. In some embodiments, the covalently modified K-Rasprotein is modulated in K-Ras subcellular localization, K-Raspost-translational processing, or K-Ras post-translationalmodifications. In some embodiments, the covalently modified K-Rasprotein contains a G12C mutation. In some embodiments, the compound iscovalently bonded to cysteine residue 12. In some embodiments, thecovalently modified K-Ras protein contains a G13C mutation. In someembodiments, the compound is covalently bonded to cysteine residue 13.In some embodiments, the K-Ras protein is bonded to a K-Ras inhibitor, amutant K-Ras inhibitor, a K-Ras G12C inhibitor, or a K-Ras G13Cinhibitor. In some embodiments, the K-Ras protein is bonded to a K-Rasmodulator, a mutant K-Ras modulator, a K-Ras G12C modulator, or a K-RasG13C modulator.

In a seventh aspect, a K-Ras protein covalently bonded to a compound,for example a compound as described herein (including modulators,inhibitors, embodiments, examples, and in Table 1, 2, 3, 4, or 5), isprovided. The compound is covalently bonded to an aspartate residue ofthe K-Ras protein. In some embodiments, the covalently modified K-Rasprotein has a modulated activity relative to a control, wherein theactivity is selected from GTPase activity, nucleotide exchange, effectorprotein binding, effector protein activation, guanine exchange factor(GEF) binding, GEF-facilitated nucleotide exchange, phosphate release,nucleotide release, nucleotide binding, K-Ras subcellular localization,K-Ras post-translational processing, and K-Ras post-translationalmodifications. In some embodiments, the covalently modified K-Rasprotein is modulated in K-Ras subcellular localization, K-Raspost-translational processing, or K-Ras post-translationalmodifications. In some embodiments, the covalently modified K-Rasprotein contains a G12D mutation. In some embodiments, the compound iscovalently bonded to aspartate residue 12. In some embodiments, thecovalently modified K-Ras protein contains a G13D mutation. In someembodiments, the compound is covalently bonded to aspartate residue 13.In some embodiments, the K-Ras protein is bonded to a K-Ras inhibitor, amutant K-Ras inhibitor, a K-Ras G12D inhibitor, or a K-Ras G13Dinhibitor. In some embodiments, the K-Ras protein is bonded to a K-Rasmodulator, a mutant K-Ras modulator, a K-Ras G12D modulator, or a K-RasG13D modulator.

In an eighth aspect, a method of identifying a covalent inhibitor ofK-Ras protein is provided. The method including contacting a K-Rasprotein with a K-Ras inhibitor test compound, allowing the K-Rasinhibitor test compound to covalently inhibit the K-Ras protein,detecting the level of covalent inhibition of the K-Ras protein, andthereby identifying a covalent inhibitor of K-Ras protein. In someembodiments of the method, the K-Ras inhibitor test compound is a Switch2—Binding Pocket covalent inhibitor test compound. In some embodiments,the K-Ras protein is a G12C mutant K-Ras protein. In some embodiments,the K-Ras protein is a G13C mutant K-Ras protein. In some embodiments,the K-Ras protein is a G12D mutant K-Ras protein. In some embodiments,the K-Ras protein is a G13D mutant K-Ras protein. In some embodiments ofthe method, wherein the K-Ras protein contacting the Switch 2—BindingPocket covalent inhibitor test compound is a mutant K-Ras (e.g. K-RasG12C, G12D, G13C, G13D), the method further includes contacting awildtype K-Ras protein with the Switch 2—Binding Pocket covalentinhibitor test compound, allowing the Switch 2—Binding Pocket covalentinhibitor test compound to inhibit the wildtype K-Ras protein, detectingthe level of inhibition of the wildtype K-Ras protein, comparing thelevel of inhibition of the wildtype K-Ras protein to the level ofcovalent inhibition of the mutant K-Ras protein (e.g. K-Ras G12C, G12D,G13C, G13D), wherein a higher level of covalent inhibition of the mutantK-Ras protein indicates the Switch 2—Binding Pocket covalent inhibitortest compound is specific for the mutant K-Ras protein. In someembodiments, the K-Ras inhibitor test compound is a Switch 2—BindingPocket covalent inhibitor test compound and the K-Ras protein is a G12Cmutant K-Ras protein. In some embodiments, the K-Ras inhibitor testcompound is a Switch 2—Binding Pocket covalent inhibitor test compoundand the K-Ras protein is a G12D mutant K-Ras protein. In someembodiments, the K-Ras inhibitor test compound is a Switch 2—BindingPocket covalent inhibitor test compound and the K-Ras protein is a G13Cmutant K-Ras protein. In some embodiments, the K-Ras inhibitor testcompound is a Switch 2—Binding Pocket covalent inhibitor test compoundand the K-Ras protein is a G13D mutant K-Ras protein. In someembodiments of the method, the Switch 2—Binding Pocket covalent testinhibitor compound does not covalently inhibit the wildtype K-Rasprotein.

In some embodiments of the above aspects, the compound binds Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) behind Switch II. In embodiments, the compound modulates theconformation of Switch II. In embodiments, the compound modulates theconformation of Switch I. In embodiments, the compound modulates theconformation of Switch I and Switch II. In embodiments, the compoundinhibits (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9,1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000,5000, 6000, 7000, 8000, 9000, 10000 fold or more) Ras (e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) nucleotide exchange (e.g. GDP for GTP or GTP for GDP) relative tothe absence of the compound. In embodiments, the compound inhibitsrelease of GDP from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the absence of thecompound. In embodiments, the compound inhibits binding of GDP to Ras(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) relative to the absence of the compound. Inembodiments, the compound inhibits binding of GTP to Ras (e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) relative to the absence of the compound. In embodiments, thecompound increases (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,0.8, 0.9, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,80, 85, 90, 95, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000,3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000 fold or more) Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) nucleotide exchange (e.g. GDP for GTP or GTP for GDP)relative to the absence of the compound. In embodiments, the compoundincreases release of GDP from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the absenceof the compound. In embodiments, the compound increases release of GTPfrom Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,K-Ras G12D, K-Ras G13D) relative to the absence of the compound. Inembodiments, the compound increases binding of GDP to Ras (e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) relative to the absence of the compound. In embodiments, thecompound inhibits binding of GTP to Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative tothe absence of the compound. In embodiments, the compound inhibitsbinding of a GTP analog (e.g. mant-dGTP) to Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)relative to the absence of the compound. In embodiments, the compoundmodulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutantRas, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid thatcontacts GTP in the absence of the compound. In embodiments, thecompound modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acidthat contacts GDP in the absence of the compound. In embodiments, thecompound modulates the conformation of a plurality of Ras (e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) amino acids that contact GTP in the absence of the compound. Inembodiments, the compound modulates the conformation of a plurality ofRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) amino acids that contact GDP in the absence of thecompound. In embodiments, the compound modulates the binding of GTPand/or GDP to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D) compared to binding in the absenceof the compound. In embodiments, the compound modulates the release ofGTP and/or GDP from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) compared to release in theabsence of the compound. In embodiments, the compound modulates theratio of the binding of GTP and GDP to Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) compared tothe ratio in the absence of the compound. In embodiments, the compoundmodulates the ratio of the rate of release of GTP and GDP from Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) compared to the ratio in the absence of the compound. Inembodiments, the compound modulates the conformation of a Ras amino acidthat contacts the gamma phosphate of GTP when GTP is bound to Ras. Inembodiments, the compound inhibits the binding of the gamma phosphate ofGTP relative to the binding in the absence of the compound. Inembodiments, the compound binds Ras (e.g. K-Ras, H-Ras, N-Ras, mutantRas, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) protein bound toGDP and, after release of the GDP, modulates the subsequent binding ofGDP or GTP to the Ras bound to the compound. In embodiments, thecompound binds Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D) protein bound to GDP and, afterrelease of the GDP, modulates the subsequent binding of GDP to the Rasbound to the compound. In embodiments, the compound binds Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) protein bound to GDP and, after release of the GDP,modulates the subsequent binding of GTP to the Ras bound to thecompound.

In embodiments, the compound inhibits proliferation of cancer cellsunder nutrient deficient conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder nutrient deficient conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder nutrient deficient conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder serum deprivation conditions relative to the absence of thecompound. In embodiments, the compound inhibits proliferation of cancercells under serum deprivation conditions relative to the absence of thecompound. In embodiments, the compound inhibits growth of cancer cellsunder conditions (e.g. local cell environment in a patient) mimickingserum deprivation relative to the absence of the compound. Inembodiments, the compound inhibits proliferation of cancer cells underconditions (e.g. local cell environment in a patient) mimicking serumdeprivation relative to the absence of the compound.

In embodiments, the compound modulates the conformation of the aminoacid corresponding to amino acid 60 in human K-Ras in a Ras protein. Inembodiments, the compound modulates the distance between the alphacarbon of the amino acid corresponding to amino acid 12 in human K-Rasand the alpha carbon of the amino acid corresponding to amino acid 60 inhuman K-Ras, in a Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D). In embodiments thecompound increases the distance between the alpha carbon of the aminoacid corresponding to amino acid 12 in human K-Ras and the alpha carbonof the amino acid corresponding to amino acid 60 in human K-Ras, in aRas protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D). In embodiments the compound increases thedistance (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9,1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3,2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7,3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1,5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5,6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9,8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3,9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6,10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8,11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2,14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4,15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6,17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8,18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0,or more angstroms) between the alpha carbon of the amino acidcorresponding to amino acid 12 in human K-Ras and the alpha carbon ofthe amino acid corresponding to amino acid 60 in human K-Ras, in a Rasprotein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,K-Ras G12D, K-Ras G13D) relative to the absence of the compound. Inembodiments the compound increases the distance (e.g. by about 0.1, 0.2,0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6,1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0,3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4,4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2,7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6,8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0,10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2,11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4,12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6,13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8,14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0,17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2,18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4,19.5, 19.6, 19.7, 19.8, 19.9, 20.0, or more angstroms) between the alphacarbon of the amino acid corresponding to amino acid 12 in human K-Rasand the alpha carbon of the amino acid corresponding to amino acid 60 inhuman K-Ras, in a Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) when bound to GDP,relative to the absence of the compound. In embodiments the compoundincreases the distance (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1,2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5,3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9,5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3,6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1,9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4,10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6,11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8,12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0,14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4,17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6,18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8,19.9, 20.0, or more angstroms) between the alpha carbon of the aminoacid corresponding to amino acid 12 in human K-Ras and the alpha carbonof the amino acid corresponding to amino acid 60 in human K-Ras, in aRas protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) when bound to GTP, compared to thedistance in the absence of the compound. In embodiments, upon binding toRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) the compound (e.g. a compound described herein,including embodiments and including a compound described in a table,example, or figure) modulates the distance between the alpha carbon ofthe amino acid corresponding to amino acid 12 in human K-Ras and thealpha carbon of the amino acid corresponding to amino acid 60 in humanK-Ras, in the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to be about 4.9 angstroms orgreater (e.g. about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9,5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3,6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1,9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4,10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6,11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8,12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0,14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4,17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6,18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8,19.9, 20.0 angstroms, or greater). In embodiments, upon binding to Ras(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) the compound (e.g. a compound described herein,including embodiments and including a compound described in a table,example, or figure) modulates the distance between the alpha carbon ofthe amino acid corresponding to amino acid 12 in human K-Ras and thealpha carbon of the amino acid corresponding to amino acid 60 in humanK-Ras, in the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to be greater than about 4.9angstroms (e.g. greater than about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6,5.7, 5.8, 5.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0,6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4,7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8,8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2,10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4,11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6,12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8,13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0,15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2,17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4,18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6,19.7, 19.8, 19.9, 20.0 angstroms, or greater). In embodiments, uponbinding to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) the compound (e.g. a compound describedherein, including embodiments and including a compound described in atable, example, or figure) modulates the distance between the alphacarbon of the amino acid corresponding to amino acid 12 in human K-Rasand the alpha carbon of the amino acid corresponding to amino acid 60 inhuman K-Ras, in the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to be 4.9 angstroms orgreater (e.g. 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0,5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4,6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8,7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2,9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5,10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7,11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9,13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1,14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3,15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5,17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7,18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9,20.0 angstroms, or greater). In embodiments, upon binding to Ras (e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) the compound (e.g. a compound described herein, includingembodiments and including a compound described in a table, example, orfigure) modulates the distance between the alpha carbon of the aminoacid corresponding to amino acid 12 in human K-Ras and the alpha carbonof the amino acid corresponding to amino acid 60 in human K-Ras, in theRas protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) to be greater than 4.9 angstroms (e.g.greater than 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0, 5.1,5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5,6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9,8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3,9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6,10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8,11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2,14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4,15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6,17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8,18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0angstroms, or greater).

In embodiments, the compound increases the flexibility of Switch Irelative to the absence of the compound. In embodiments, the compoundincreases the disorder of Switch I relative to the absence of thecompound. In embodiments, the compound inhibits the binding of Ras((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) to another protein. In embodiments, the compoundinhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras,K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to another protein,wherein the binding is dependent on Ras binding to GTP. In embodiments,the compound inhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to anotherprotein, wherein the binding is dependent on Ras binding to GDP. Inembodiments, the compound inhibits the binding of Ras ((e.g. K-Ras,H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-RasG13D) to Raf (e.g. Raf1). In embodiments, the compound inhibits thebinding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-RasG13C, K-Ras G12D, K-Ras G13D) to SOS. In embodiments, the compoundinhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras) to aGEF. In embodiments, the compound inhibits the binding of Ras ((e.g.K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D,K-Ras G13D) to PI3K. In embodiments, the compound modulates metalbinding near the nucleotide binding site. In embodiments, the compoundmodulates the conformation of the Ras metal binding site near thenucleotide binding site. In embodiments, the compound modulates theconformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid relative to theconformation in the absence of the compound, wherein the Ras amino acidconformation is also modulated by a Ras G60 mutation. In embodiments,the compound modulates the conformation of a Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) aminoacid relative to the conformation in the absence of the compound,wherein the Ras amino acid conformation is also modulated by a Ras G60Amutation. In embodiments, the compound modulates the conformation of aRas (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-RasG12D, K-Ras G13D) amino acid relative to the conformation in the absenceof the compound, wherein the Ras amino acid conformation is alsomodulated by a Ras T35 mutation. In embodiments, the compound modulatesthe conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-RasG12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid relative to theconformation in the absence of the compound, wherein the Ras amino acidconformation is also modulated by a Ras T35S mutation. In embodiments,the compound modulates the conformation of a Ras (e.g. K-Ras, H-Ras,N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) aminoacid relative to the conformation in the absence of the compound,wherein the Ras amino acid conformation is also modulated by a mutationof the Ras amino acid corresponding to K-Ras G60. In embodiments, thecompound modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acidrelative to the conformation in the absence of the compound, wherein theRas amino acid conformation is also modulated by a mutation of the Rasamino acid corresponding to K-Ras T35.

The pharmaceutical compositions include optical isomers, diastereomers,or pharmaceutically acceptable salts of the modulators disclosed herein.The compound included in the pharmaceutical composition may becovalently attached to a carrier moiety, as described above.Alternatively, the compound included in the pharmaceutical compositionis not covalently linked to a carrier moiety.

In a ninth aspect, a Ras protein (e.g. K-Ras, N-Ras, H-Ras, or anotherRas protein described herein) covalently bonded (e.g. reversibly orirreversibly) to a compound, for example a compound as described herein(including modulators, inhibitors, embodiments, examples, and anycompound in Table 1, 2, 3, 4, or 5), is provided. In some embodiments,the compound is covalently bonded to a cysteine, aspartate, lysine,tyrosine or glutamate residue of the Ras protein (e.g. K-Ras, N-Ras,H-Ras, or another Ras protein described herein). In some embodiments,the compound is a modulator. In some embodiments, the compound is amodulator such as an inhibitor. In some embodiments, the compound is aRas modulator. In some embodiments, the compound is a Ras inhibitor.

The compounds of the invention (i.e. compounds described herein,including embodiments, examples, compounds of Table 1, 2, 3, 4, or 5)can be administered alone or can be coadministered to the patient.Coadministration is meant to include simultaneous or sequentialadministration of the compounds individually or in combination (morethan one compound). Thus, the preparations can also be combined, whendesired, with other active substances (e.g. to reduce metabolicdegradation).

The compounds of the present invention can be prepared and administeredin a wide variety of oral, parenteral and topical dosage forms. Oralpreparations include tablets, pills, powder, dragees, capsules, liquids,lozenges, cachets, gels, syrups, slurries, suspensions, etc., suitablefor ingestion by the patient. The compounds of the present invention canalso be administered by injection, that is, intravenously,intramuscularly, intracutaneously, subcutaneously, intraduodenally, orintraperitoneally. Also, the compounds described herein can beadministered by inhalation, for example, intranasally. Additionally, thecompounds of the present invention can be administered transdermally. Itis also envisioned that multiple routes of administration (e.g.,intramuscular, oral, transdermal) can be used to administer thecompounds of the invention. Accordingly, the present invention alsoprovides pharmaceutical compositions comprising a pharmaceuticallyacceptable excipient and one or more compounds of the invention.

For preparing pharmaceutical compositions from the compounds of thepresent invention, pharmaceutically acceptable carriers can be eithersolid or liquid. Solid form preparations include powders, tablets,pills, capsules, cachets, suppositories, and dispersible granules. Asolid carrier can be one or more substances, that may also act asdiluents, flavoring agents, binders, preservatives, tabletdisintegrating agents, or an encapsulating material.

In powders, the carrier is a finely divided solid in a mixture with thefinely divided active component (e.g. a compound provided herein). Intablets, the active component is mixed with the carrier having thenecessary binding properties in suitable proportions and compacted inthe shape and size desired. The powders and tablets preferably containfrom 5% to 70% of the active compound.

Suitable solid excipients include, but are not limited to, magnesiumcarbonate; magnesium stearate; talc; pectin; dextrin; starch;tragacanth; a low melting wax; cocoa butter; carbohydrates; sugarsincluding, but not limited to, lactose, sucrose, mannitol, or sorbitol,starch from corn, wheat, rice, potato, or other plants; cellulose suchas methyl cellulose, hydroxypropylmethyl-cellulose, or sodiumcarboxymethylcellulose; and gums including arabic and tragacanth; aswell as proteins including, but not limited to, gelatin and collagen. Ifdesired, disintegrating or solubilizing agents may be added, such as thecross-linked polyvinyl pyrrolidone, agar, alginic acid, or a saltthereof, such as sodium alginate.

Dragee cores are provided with suitable coatings such as concentratedsugar solutions, which may also contain gum arabic, talc,polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titaniumdioxide, lacquer solutions, and suitable organic solvents or solventmixtures. Dyestuffs or pigments may be added to the tablets or drageecoatings for product identification or to characterize the quantity ofactive compound (i.e., dosage). Pharmaceutical preparations of theinvention can also be used orally using, for example, push-fit capsulesmade of gelatin, as well as soft, sealed capsules made of gelatin and acoating such as glycerol or sorbitol.

For preparing suppositories, a low melting wax, such as a mixture offatty acid glycerides or cocoa butter, is first melted and the activecomponent is dispersed homogeneously therein, as by stirring. The moltenhomogeneous mixture is then poured into convenient sized molds, allowedto cool, and thereby to solidify.

Liquid form preparations include solutions, suspensions, and emulsions,for example, water or water/propylene glycol solutions. For parenteralinjection, liquid preparations can be formulated in solution in aqueouspolyethylene glycol solution.

When parenteral application is needed or desired, particularly suitableadmixtures for the compounds of the invention are injectable, sterilesolutions, preferably oily or aqueous solutions, as well as suspensions,emulsions, or implants, including suppositories. In particular, carriersfor parenteral administration include aqueous solutions of dextrose,saline, pure water, ethanol, glycerol, propylene glycol, peanut oil,sesame oil, polyoxyethylene-block polymers, and the like. Ampules areconvenient unit dosages. The compounds of the invention can also beincorporated into liposomes or administered via transdermal pumps orpatches. Pharmaceutical admixtures suitable for use in the presentinvention are well-known to those of skill in the art and are described,for example, in Pharmaceutical Sciences (17th Ed., Mack Pub. Co.,Easton, Pa.) and WO 96/05309, the teachings of both of which are herebyincorporated by reference.

Aqueous solutions suitable for oral use can be prepared by dissolvingthe active component (e.g. compounds described herein, includingembodiments, examples, compounds of Table 1, 2, 3, 4, or 5) in water andadding suitable colorants, flavors, stabilizers, and thickening agentsas desired. Aqueous suspensions suitable for oral use can be made bydispersing the finely divided active component in water with viscousmaterial, such as natural or synthetic gums, resins, methylcellulose,sodium carboxymethylcellulose, hydroxypropylmethylcellulose, sodiumalginate, polyvinylpyrrolidone, gum tragacanth and gum acacia, anddispersing or wetting agents such as a naturally occurring phosphatide(e.g., lecithin), a condensation product of an alkylene oxide with afatty acid (e.g., polyoxyethylene stearate), a condensation product ofethylene oxide with a long chain aliphatic alcohol (e.g.,heptadecaethylene oxycetanol), a condensation product of ethylene oxidewith a partial ester derived from a fatty acid and a hexitol (e.g.,polyoxyethylene sorbitol mono-oleate), or a condensation product ofethylene oxide with a partial ester derived from fatty acid and ahexitol anhydride (e.g., polyoxyethylene sorbitan mono-oleate). Theaqueous suspension can also contain one or more preservatives such asethyl or n-propyl p-hydroxybenzoate, one or more coloring agents, one ormore flavoring agents and one or more sweetening agents, such assucrose, aspartame or saccharin. Formulations can be adjusted forosmolarity.

Also included are solid form preparations that are intended to beconverted, shortly before use, to liquid form preparations for oraladministration. Such liquid forms include solutions, suspensions, andemulsions. These preparations may contain, in addition to the activecomponent, colorants, flavors, stabilizers, buffers, artificial andnatural sweeteners, dispersants, thickeners, solubilizing agents, andthe like.

Oil suspensions can contain a thickening agent, such as beeswax, hardparaffin or cetyl alcohol. Sweetening agents can be added to provide apalatable oral preparation, such as glycerol, sorbitol or sucrose. Theseformulations can be preserved by the addition of an antioxidant such asascorbic acid. As an example of an injectable oil vehicle, see Minto, J.Pharmacol. Exp. Ther. 281:93-102, 1997. The pharmaceutical formulationsof the invention can also be in the form of oil-in-water emulsions. Theoily phase can be a vegetable oil or a mineral oil, described above, ora mixture of these. Suitable emulsifying agents includenaturally-occurring gums, such as gum acacia and gum tragacanth,naturally occurring phosphatides, such as soybean lecithin, esters orpartial esters derived from fatty acids and hexitol anhydrides, such assorbitan mono-oleate, and condensation products of these partial esterswith ethylene oxide, such as polyoxyethylene sorbitan mono-oleate. Theemulsion can also contain sweetening agents and flavoring agents, as inthe formulation of syrups and elixirs. Such formulations can alsocontain a demulcent, a preservative, or a coloring agent.

The pharmaceutical preparation is preferably in unit dosage form. Insuch form the preparation is subdivided into unit doses containingappropriate quantities of the active component. The unit dosage form canbe a packaged preparation, the package containing discrete quantities ofpreparation, such as packeted tablets, capsules, and powders in vials orampoules. Also, the unit dosage form can be a capsule, tablet, cachet,or lozenge itself, or it can be the appropriate number of any of thesein packaged form.

The quantity of active component in a unit dose preparation may bevaried or adjusted from 0.1 mg to 10000 mg, more typically 1.0 mg to1000 mg, most typically 10 mg to 500 mg, according to the particularapplication and the potency of the active component. The compositioncan, if desired, also contain other compatible therapeutic agents.

Some compounds may have limited solubility in water and therefore mayrequire a surfactant or other appropriate co-solvent in the composition.Such co-solvents include: Polysorbate 20, 60 and 80; Pluronic F-68, F-84and P-103; cyclodextrin; polyoxyl 35 castor oil; or other agents knownto those skilled in the art. Such co-solvents are typically employed ata level between about 0.01% and about 2% by weight.

Viscosity greater than that of simple aqueous solutions may be desirableto decrease variability in dispensing the formulations, to decreasephysical separation of components of a suspension or emulsion offormulation and/or otherwise to improve the formulation. Such viscositybuilding agents include, for example, polyvinyl alcohol, polyvinylpyrrolidone, methyl cellulose, hydroxy propyl methylcellulose,hydroxyethyl cellulose, carboxymethyl cellulose, hydroxy propylcellulose, chondroitin sulfate and salts thereof, hyaluronic acid andsalts thereof, combinations of the foregoing, and other agents known tothose skilled in the art. Such agents are typically employed at a levelbetween about 0.01% and about 2% by weight. Determination of acceptableamounts of any of the above adjuvants is readily ascertained by oneskilled in the art.

The compositions of the present invention may additionally includecomponents to provide sustained release and/or comfort. Such componentsinclude high molecular weight, anionic mucomimetic polymers, gellingpolysaccharides and finely-divided drug carrier substrates. Thesecomponents are discussed in greater detail in U.S. Pat. Nos. 4,911,920;5,403,841; 5,212,162; and 4,861,760. The entire contents of thesepatents are incorporated herein by reference in their entirety for allpurposes.

Pharmaceutical compositions provided by the present invention includecompositions wherein the active ingredient (e.g. compounds describedherein, including embodiments, examples, compounds of Table 1, 2, 3, 4,or 5) is contained in a therapeutically effective amount, i.e., in anamount effective to achieve its intended purpose. The actual amounteffective for a particular application will depend, inter alia, on thecondition being treated. When administered in methods to treat adisease, such compositions will contain an amount of active ingredienteffective to achieve the desired result, e.g., modulating the activityof a target molecule (e.g. a Ras, K-Ras, K-Ras G12C, K-Ras G12D, K-RasG13C, K-Ras G13D, a mutant K-Ras, an activated K-Ras), and/or reducing,eliminating, or slowing the progression of disease symptoms (e.g. cancergrowth or metastasis). Determination of a therapeutically effectiveamount of a compound of the invention is well within the capabilities ofthose skilled in the art, especially in light of the detailed disclosureherein.

The dosage and frequency (single or multiple doses) administered to amammal can vary depending upon a variety of factors, for example,whether the mammal suffers from another disease, and its route ofadministration; size, age, sex, health, body weight, body mass index,and diet of the recipient; nature and extent of symptoms of the diseasebeing treated (e.g. lung cancer, NSCL cancer, colon cancer, colorectalcancer, breast cancer, pancreatic cancer, leukemia), kind of concurrenttreatment, complications from the disease being treated or otherhealth-related problems. Other therapeutic regimens or agents can beused in conjunction with the methods and compounds of Applicants'invention. Adjustment and manipulation of established dosages (e.g.,frequency and duration) are well within the ability of those skilled inthe art.

For any compound described herein, the therapeutically effective amountcan be initially determined from cell culture assays. Targetconcentrations will be those concentrations of active compound(s) thatare capable of achieving the methods described herein, as measured usingthe methods described herein or known in the art.

As is well known in the art, therapeutically effective amounts for usein humans can also be determined from animal models. For example, a dosefor humans can be formulated to achieve a concentration that has beenfound to be effective in animals. The dosage in humans can be adjustedby monitoring compounds effectiveness and adjusting the dosage upwardsor downwards, as described above. Adjusting the dose to achieve maximalefficacy in humans based on the methods described above and othermethods is well within the capabilities of the ordinarily skilledartisan.

Dosages may be varied depending upon the requirements of the patient andthe compound being employed. The dose administered to a patient, in thecontext of the present invention should be sufficient to effect abeneficial therapeutic response in the patient over time. The size ofthe dose also will be determined by the existence, nature, and extent ofany adverse side-effects. Determination of the proper dosage for aparticular situation is within the skill of the practitioner. Generally,treatment is initiated with smaller dosages which are less than theoptimum dose of the compound. Thereafter, the dosage is increased bysmall increments until the optimum effect under circumstances isreached. In one embodiment, the dosage range is 0.001% to 10% w/v. Inanother embodiment, the dosage range is 0.1% to 5% w/v.

Dosage amounts and intervals can be adjusted individually to providelevels of the administered compound effective for the particularclinical indication being treated. This will provide a therapeuticregimen that is commensurate with the severity of the individual'sdisease state.

Utilizing the teachings provided herein, an effective prophylactic ortherapeutic treatment regimen can be planned that does not causesubstantial toxicity and yet is effective to treat the clinical symptomsdemonstrated by the particular patient. This planning should involve thecareful choice of active compound by considering factors such ascompound potency, relative bioavailability, patient body weight,presence and severity of adverse side effects, preferred mode ofadministration and the toxicity profile of the selected agent.

The ratio between toxicity and therapeutic effect for a particularcompound is its therapeutic index and can be expressed as the ratiobetween LD₅₀ (the amount of compound lethal in 50% of the population)and ED₅₀ (the amount of compound effective in 50% of the population).Compounds that exhibit high therapeutic indices are preferred.Therapeutic index data obtained from cell culture assays and/or animalstudies can be used in formulating a range of dosages for use in humans.The dosage of such compounds preferably lies within a range of plasmaconcentrations that include the ED₅₀ with little or no toxicity. Thedosage may vary within this range depending upon the dosage formemployed and the route of administration utilized. See, e.g. Fingl etal., In: THE PHARMACOLOGICAL BASIS OF THERAPEUTICS, Ch. 1, p. 1, 1975.The exact formulation, route of administration and dosage can be chosenby the individual physician in view of the patient's condition and theparticular method in which the compound is used.

Administration

The compositions of the present invention can be delivered bytransdermally, by a topical route, formulated as applicator sticks,solutions, suspensions, emulsions, gels, creams, ointments, pastes,jellies, paints, powders, and aerosols. For therapeutic applications,the compounds or drugs of the present invention can be administeredalone or co-administered in combination with conventional chemotherapy,radiotherapy, hormonal therapy, and/or immunotherapy.

The compositions of the present invention can also be delivered asmicrospheres for slow release in the body. For example, microspheres canbe administered via intradermal injection of drug-containingmicrospheres, which slowly release subcutaneously (see Rao, J BiomaterSci. Polym. Ed. 7:623-645, 1995; as biodegradable and injectable gelformulations (see, e.g., Gao Pharm. Res. 12:857-863, 1995); or, asmicrospheres for oral administration (see, e.g., Eyles, J. Pharm.Pharmacol. 49:669-674, 1997). Both transdermal and intradermal routesafford constant delivery for weeks or months.

The pharmaceutical compositions of the present invention can be providedas a salt and can be formed with many acids, including but not limitedto hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic,etc. Pharmaceutical compositions described herein may be salts of acompound or composition which are prepared with relatively nontoxicacids or bases, depending on the particular substituents found on thecompounds described herein. When compounds of the present inventioncontain relatively acidic functionalities, base addition salts can beobtained by contacting the neutral form of such compounds with asufficient amount of the desired base, either neat or in a suitableinert solvent. Examples of pharmaceutically acceptable base additionsalts include sodium, potassium, calcium, ammonium, organic amino, ormagnesium salt, or a similar salt. When compounds of the presentinvention contain relatively basic functionalities, acid addition saltscan be obtained by contacting the neutral form of such compounds with asufficient amount of the desired acid, either neat or in a suitableinert solvent. Examples of pharmaceutically acceptable acid additionsalts include those derived from inorganic acids like hydrochloric,hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric,monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,monohydrogensulfuric, hydriodic, or phosphorous acids and the like, aswell as the salts derived from relatively nontoxic organic acids likeacetic, propionic, isobutyric, maleic, malonic, benzoic, succinic,suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic,p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Alsoincluded are salts of amino acids such as arginate and the like, andsalts of organic acids like glucuronic or galactunoric acids and thelike (see, e.g., Berge et al., Journal of Pharmaceutical Science 66:1-19(1977)). Certain specific compounds of the present invention containboth basic and acidic functionalities that allow the compounds to beconverted into either base or acid addition salts. Otherpharmaceutically acceptable carriers known to those of skill in the artare suitable for the present invention. Salts tend to be more soluble inaqueous or other protonic solvents that are the corresponding free baseforms. In other cases, the preparation may be a lyophilized powder in 1mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5to 5.5, that is combined with buffer prior to use.

The neutral forms of the compounds may be regenerated by contacting thesalt with a base or acid and isolating the parent compound in theconventional manner. The parent form of the compound differs from thevarious salt forms in certain physical properties, such as solubility inpolar solvents, but otherwise the salts are equivalent to the parentform of the compound for the purposes of the present invention.

Certain compositions described herein or Ras inhibitor compounds of thepresent invention can exist in unsolvated forms as well as solvatedforms, including hydrated forms. In general, the solvated forms areequivalent to unsolvated forms and are intended to be encompassed withinthe scope of the present invention. Certain Ras inhibitor compounds ofthe present invention may exist in multiple crystalline or amorphousforms. In general, all physical forms are equivalent for the usescontemplated by the present invention and are intended to be within thescope of the present invention.

In another embodiment, the compositions of the present invention areuseful for parenteral administration, such as intravenous (IV)administration or administration into a body cavity or lumen of anorgan. The formulations for administration will commonly comprise asolution of the compositions of the present invention dissolved in apharmaceutically acceptable carrier. Among the acceptable vehicles andsolvents that can be employed are water and Ringer's solution, anisotonic sodium chloride. In addition, sterile fixed oils canconventionally be employed as a solvent or suspending medium. For thispurpose any bland fixed oil can be employed including synthetic mono- ordiglycerides. In addition, fatty acids such as oleic acid can likewisebe used in the preparation of injectables. These solutions are sterileand generally free of undesirable matter. These formulations may besterilized by conventional, well known sterilization techniques. Theformulations may contain pharmaceutically acceptable auxiliarysubstances as required to approximate physiological conditions such aspH adjusting and buffering agents, toxicity adjusting agents, e.g.,sodium acetate, sodium chloride, potassium chloride, calcium chloride,sodium lactate and the like. The concentration of the compositions ofthe present invention in these formulations can vary widely, and will beselected primarily based on fluid volumes, viscosities, body weight, andthe like, in accordance with the particular mode of administrationselected and the patient's needs. For IV administration, the formulationcan be a sterile injectable preparation, such as a sterile injectableaqueous or oleaginous suspension. This suspension can be formulatedaccording to the known art using those suitable dispersing or wettingagents and suspending agents. The sterile injectable preparation canalso be a sterile injectable solution or suspension in a nontoxicparenterally-acceptable diluent or solvent, such as a solution of1,3-butanediol.

In another embodiment, the formulations of the compositions of thepresent invention can be delivered by the use of liposomes which fusewith the cellular membrane or are endocytosed, i.e., by employingreceptor ligands attached to the liposome, that bind to surface membraneprotein receptors of the cell resulting in endocytosis. By usingliposomes, particularly where the liposome surface carries receptorligands specific for target cells, or are otherwise preferentiallydirected to a specific organ, one can focus the delivery of thecompositions of the present invention into the target cells in vivo.(See, e.g., Al-Muhammed, J. Microencapsul. 13:293-306, 1996; Chonn,Curr. Opin. Biotechnol. 6:698-708, 1995; Ostro, Am. J. Hosp. Pharm.46:1576-1587, 1989).

The compounds described herein can be used in combination with oneanother, with other active agents known to be useful in treating adisease associated with cells expressing a particular Ras, K-Ras, mutantK-Ras (e.g. cancer), or with adjunctive agents that may not be effectivealone, but may contribute to the efficacy of the active agent.

In some embodiments, co-administration includes administering one activeagent within 0.5, 1, 2, 4, 6, 8, 10, 12, 16, 20, or 24 hours of a secondactive agent. Co-administration includes administering two active agentssimultaneously, approximately simultaneously (e.g., within about 1, 5,10, 15, 20, or 30 minutes of each other), or sequentially in any order.In some embodiments, co-administration can be accomplished byco-formulation, i.e., preparing a single pharmaceutical compositionincluding both active agents. In other embodiments, the active agentscan be formulated separately. In another embodiment, the active and/oradjunctive agents may be linked or conjugated to one another.

As a non-limiting example, the compounds described herein can beco-administered with conventional chemotherapeutic agents includingalkylating agents (e.g., cyclophosphamide, ifosfamide, chlorambucil,busulfan, melphalan, mechlorethamine, uramustine, thiotepa,nitrosoureas, etc.), anti-metabolites (e.g., 5-fluorouracil,azathioprine, methotrexate, leucovorin, capecitabine, cytarabine,floxuridine, fludarabine, gemcitabine, pemetrexed, raltitrexed, etc.),plant alkaloids (e.g., vincristine, vinblastine, vinorelbine, vindesine,podophyllotoxin, paclitaxel, docetaxel, etc.), topoisomerase inhibitors(e.g., irinotecan, topotecan, amsacrine, etoposide (VP16), etoposidephosphate, teniposide, etc.), antitumor antibiotics (e.g., doxorubicin,adriamycin, daunorubicin, epirubicin, actinomycin, bleomycin, mitomycin,mitoxantrone, plicamycin, etc.), platinum-based compounds (e.g.cisplatin, oxaloplatin, carboplatin, etc.), and the like.

The compounds described herein can also be co-administered withconventional hormonal therapeutic agents including, but not limited to,steroids (e.g., dexamethasone), finasteride, aromatase inhibitors,tamoxifen, and gonadotropin-releasing hormone agonists (GnRH) such asgoserelin.

Additionally, the compounds described herein can be co-administered withconventional immunotherapeutic agents including, but not limited to,immunostimulants (e.g., Bacillus Calmette-Guérin (BCG), levamisole,interleukin-2, alpha-interferon, etc.), monoclonal antibodies (e.g.,anti-CD20, anti-HER2, anti-CD52, anti-HLA-DR, and anti-VEGF monoclonalantibodies), immunotoxins (e.g., anti-CD33 monoclonalantibody-calicheamicin conjugate, anti-CD22 monoclonalantibody-pseudomonas exotoxin conjugate, etc.), and radioimmunotherapy(e.g., anti-CD20 monoclonal antibody conjugated to ¹¹¹In, ⁹⁰Y, or ¹³¹I,etc.).

In a further embodiment, the compounds described herein can beco-administered with conventional radiotherapeutic agents including, butnot limited to, radionuclides such as ⁴⁷Sc, ⁶⁴Cu, ⁶⁷Cu, ⁸⁹Sr, ⁸⁶Y, ⁸⁷Y,⁹⁰Y, ¹⁰⁵Rh, ¹¹¹Ag, ¹¹¹In, ^(117m)Sn, ¹⁴⁹Pm, ¹⁵³Sm, ¹⁶⁶Ho, ¹⁷⁷Lu, ¹⁸⁶Re,¹⁸⁸Re, ²¹¹At, and ²¹²Bi, optionally conjugated to antibodies directedagainst tumor antigens.

The pharmaceutical compositions of the present invention may besterilized by conventional, well-known sterilization techniques or maybe produced under sterile conditions. Aqueous solutions can be packagedfor use or filtered under aseptic conditions and lyophilized, thelyophilized preparation being combined with a sterile aqueous solutionprior to administration. The compositions can contain pharmaceuticallyacceptable auxiliary substances as required to approximate physiologicalconditions, such as pH adjusting and buffering agents, tonicityadjusting agents, wetting agents, and the like, e.g., sodium acetate,sodium lactate, sodium chloride, potassium chloride, calcium chloride,sorbitan monolaurate, and triethanolamine oleate.

Formulations suitable for oral administration can comprise: (a) liquidsolutions, such as an effective amount of a packaged compound or drugsuspended in diluents, e.g., water, saline, or PEG 400; (b) capsules,sachets, or tablets, each containing a predetermined amount of a Rasinhibitor compound or drug, as liquids, solids, granules or gelatin; (c)suspensions in an appropriate liquid; and (d) suitable emulsions. Tabletforms can include one or more of lactose, sucrose, mannitol, sorbitol,calcium phosphates, corn starch, potato starch, microcrystallinecellulose, gelatin, colloidal silicon dioxide, talc, magnesium stearate,stearic acid, and other excipients, colorants, fillers, binders,diluents, buffering agents, moistening agents, preservatives, flavoringagents, dyes, disintegrating agents, and pharmaceutically compatiblecarriers. Lozenge forms can comprise a Ras inhibitor compound or drug ina flavor, e.g., sucrose, as well as pastilles comprising the Rasinhibitor compound in an inert base, such as gelatin and glycerin orsucrose and acacia emulsions, gels, and the like, containing, inaddition to the Ras inhibitor, carriers known in the art.

The compound of choice, alone or in combination with other suitablecomponents, can be made into aerosol formulations (i.e., they can be“nebulized”) to be administered via inhalation. Aerosol formulations canbe placed into pressurized acceptable propellants, such asdichlorodifluoromethane, propane, nitrogen, and the like.

Suitable formulations for rectal administration include, for example,suppositories, which comprises an effective amount of a packaged Rasinhibitor compound or drug with a suppository base. Suitable suppositorybases include natural or synthetic triglycerides or paraffinhydrocarbons. In addition, it is also possible to use gelatin rectalcapsules which contain a combination of the Ras inhibitor compound ordrug of choice with a base, including, for example, liquidtriglycerides, polyethylene glycols, and paraffin hydrocarbons.

Formulations suitable for parenteral administration, such as, forexample, by intraarticular (in the joints), intravenous, intramuscular,intratumoral, intradermal, intraperitoneal, and subcutaneous routes,include aqueous and non-aqueous, isotonic sterile injection solutions,which can contain antioxidants, buffers, bacteriostats, and solutes thatrender the formulation isotonic with the blood of the intendedrecipient, and aqueous and non-aqueous sterile suspensions that caninclude suspending agents, solubilizers, thickening agents, stabilizers,and preservatives. Injection solutions and suspensions can also beprepared from sterile powders, granules, and tablets. In the practice ofthe present invention, compositions can be administered, for example, byintravenous infusion, orally, topically, intraperitoneally,intravesically, or intrathecally. Parenteral administration, oraladministration, and intravenous administration are the preferred methodsof administration. The formulations of compounds can be presented inunit-dose or multi-dose sealed containers, such as ampoules and vials.

The pharmaceutical preparation is preferably in unit dosage form. Insuch form the preparation is subdivided into unit doses containingappropriate quantities of the active component, e.g., a Ras inhibitorcompound. The unit dosage form can be a packaged preparation, thepackage containing discrete quantities of preparation, such as packetedtablets, capsules, and powders in vials or ampoules. Also, the unitdosage form can be a capsule, tablet, cachet, or lozenge itself, or itcan be the appropriate number of any of these in packaged form. Thecomposition can, if desired, also contain other compatible therapeuticagents.

In therapeutic use for the treatment of cancer, compound utilized in thepharmaceutical compositions of the present invention may be administeredat the initial dosage of about 0.001 mg/kg to about 1000 mg/kg daily. Adaily dose range of about 0.01 mg/kg to about 500 mg/kg, or about 0.1mg/kg to about 200 mg/kg, or about 1 mg/kg to about 100 mg/kg, or about10 mg/kg to about 50 mg/kg, can be used. The dosages, however, may bevaried depending upon the requirements of the patient, the severity ofthe condition being treated, and the compound or drug being employed.For example, dosages can be empirically determined considering the typeand stage of cancer diagnosed in a particular patient. The doseadministered to a patient, in the context of the present invention,should be sufficient to affect a beneficial therapeutic response in thepatient over time. The size of the dose will also be determined by theexistence, nature, and extent of any adverse side-effects that accompanythe administration of a compound in a particular patient. Determinationof the proper dosage for a particular situation is within the skill ofthe practitioner. Generally, treatment is initiated with smaller dosageswhich are less than the optimum dose of the compound. Thereafter, thedosage is increased by small increments until the optimum effect undercircumstances is reached. For convenience, the total daily dosage may bedivided and administered in portions during the day, if desired.

The compounds described herein can be used in combination with oneanother, with other active agents known to be useful in treating canceror with adjunctive agents that may not be effective alone, but maycontribute to the efficacy of the active agent.

Kits/Articles of Manufacture

For use in the methods and/or applications (e.g. therapeuticapplications) described herein, kits and articles of manufacture arealso provided. In some embodiments, such kits comprise a carrier,package, or container that is compartmentalized to receive one or morecontainers such as vials, tubes, and the like, each of the container(s)comprising one of the separate elements to be used in a method describedherein. Suitable containers include, for example, bottles, vials,syringes, and test tubes. The containers are formed from a variety ofmaterials such as glass or plastic.

The articles of manufacture provided herein contain packaging materials.Packaging materials for use in packaging pharmaceutical products includethose found in, e.g., U.S. Pat. Nos. 5,323,907, 5,052,558 and 5,033,252.Examples of pharmaceutical packaging materials include, but are notlimited to, blister packs, bottles, tubes, inhalers, pumps, bags, vials,containers, syringes, bottles, and any packaging material suitable for aselected formulation and intended mode of administration and treatment.For example, the container(s) includes one or more compounds describedherein, optionally in a composition or in combination with another agentas disclosed herein. The container(s) optionally have a sterile accessport (for example the container is an intravenous solution bag or a vialhaving a stopper pierceable by a hypodermic injection needle). Such kitsoptionally comprising a compound with an identifying description orlabel or instructions relating to its use in the methods describedherein.

For example, a kit may include one or more additional containers, eachwith one or more of various materials (such as reagents, optionally inconcentrated form, and/or devices) desirable from a commercial and userstandpoint for use of a compound described herein. Non-limiting examplesof such materials include, but not limited to, buffers, diluents,filters, needles, syringes; carrier, package, container, vial and/ortube labels listing contents and/or instructions for use, and packageinserts with instructions for use. A set of instructions may also beincluded. A label is optionally on or associated with the container. Forexample, a label is on a container when letters, numbers or othercharacters forming the label are attached, molded or etched into thecontainer itself, a label is associated with a container when it ispresent within a receptacle or carrier that also holds the container,e.g., as a package insert. In addition, a label may be used to indicatethat the contents are to be used for a specific therapeutic application.In addition, the label may indicate directions for use of the contents,such as in the methods described herein. In certain embodiments, thepharmaceutical compositions is presented in a pack or dispenser devicewhich contains one or more unit dosage forms containing a compoundprovided herein. The pack for example contains metal or plastic foil,such as a blister pack. Or, the pack or dispenser device may beaccompanied by instructions for administration. Or, the pack ordispenser may be accompanied with a notice associated with the containerin form prescribed by a governmental agency regulating the manufacture,use, or sale of pharmaceuticals, which notice is reflective of approvalby the agency of the form of the drug for human or veterinaryadministration. Such notice, for example, is the labeling approved bythe U.S. Food and Drug Administration for prescription drugs, or theapproved product insert. In some embodiments, compositions containing acompound provided herein formulated in a compatible pharmaceuticalcarrier are prepared, placed in an appropriate container, and labeledfor treatment of an indicated condition.

ADDITIONAL EMBODIMENTS

1. A compound having the formula: R¹-L¹-L²-L³-E wherein, R¹ is a Switch2—Binding Pocket binding moiety; L¹ is a bond or a divalent radicalchemical linker; L² is a bond or a divalent radical chemical linker; L³is a bond or a divalent radical chemical linker; E is an electrophilicchemical moiety capable of forming a covalent bond with a K-Ras cysteineresidue or a K-Ras aspartate residue.

2. The compound of embodiment 1, wherein R¹ is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl.

3. The compound of embodiment 1, wherein R¹ is substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl.

4. The compound of embodiment 1, wherein R¹ is substituted orunsubstituted aryl or substituted or unsubstituted heteroaryl.

5. The compound of embodiment 1, wherein R¹ is substituted orunsubstituted fused ring aryl or substituted or unsubstituted fused ringheteroaryl.

6. The compound of embodiment 1, wherein R¹ is R³-substituted orunsubstituted aryl or R³-substituted or unsubstituted heteroaryl;wherein, R³ is independently hydrogen, oxo, halogen, —CX₃, —CN, —SO₂Cl,—SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸,—N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰,—NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; Two adjacent R³ substituents may optionally bejoined to form a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. Two R³ substituents bonded tothe same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R⁷ and R⁸ substituents bonded to the samenitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; m and v are independently 1 or 2; n is independently aninteger from 0 to 4; X is independently —Cl, —Br, —I, or —F.

7. The compound of embodiment 1, wherein R¹ is:

wherein, R³ is independently hydrogen, oxo, halogen, —CX₃, —CN, —SO₂Cl,—SO_(n)R¹, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸,—N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰,—NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; Two adjacent R³ substituents may optionally bejoined to form a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl. Two R³ substituents bonded tothe same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R⁷ and R⁸ substituents bonded to the samenitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; m and v are independently 1 or 2; n is independently aninteger from 0 to 4; X is independently —C1, —Br, —I, or —F; e2 isindependently an integer from 0 to 2; e3 is independently an integerfrom 0 to 3; e4 is independently an integer from 0 to 4; e5 isindependently an integer from 0 to 5; e6 is independently an integerfrom 0 to 6; e7 is independently an integer from 0 to 7.

8. The compound of embodiment 1, wherein R¹ is R³-substituted pyridinyl,R³-substituted pyrimidinyl, R³-substituted thiophenyl, R³-substitutedfuranyl, R³-substituted indolyl, R³-substituted benzoxadiazolyl,R³-substituted benzodioxolyl, R³-substituted benzodioxanyl,R³-substituted thianaphthanyl, R³-substituted pyrrolopyridinyl,R³-substituted indazolyl, R³-substituted quinolinyl, R³-substitutedquinoxalinyl, R³-substituted pyridopyrazinyl, R³-substitutedquinazolinonyl, R³-substituted benzoisoxazolyl, R³-substitutedimidazopyridinyl, R³-substituted benzofuranyl, R³-substitutedbenzothiophenyl, R³-substituted phenyl, R³-substituted naphthyl,R³-substituted biphenyl, R³-substituted pyrrolyl, R³-substitutedpyrazolyl, R³-substituted imidazolyl, R³-substituted pyrazinyl,R³-substituted oxazolyl, R³-substituted isoxazolyl, R³-substitutedthiazolyl, R³-substituted furylthienyl, R³-substituted pyridyl,R³-substituted pyrimidyl, R³-substituted benzothiazolyl, R³-substitutedpurinyl, R³-substituted benzimidazolyl, R³-substituted isoquinolyl,R³-substituted thiadiazolyl, R³-substituted oxadiazolyl, R³-substitutedpyrrolyl, R³-substituted diazolyl, R³-substituted triazolyl,R³-substituted tetrazolyl, R³-substituted benzothiadiazolyl,R³-substituted isothiazolyl, R³-substituted pyrazolopyrimidinyl,R³-substituted pyrrolopyrimidinyl, R³-substituted benzotriazolyl, orR³-substituted quinolyl; R³ is independently hydrogen, oxo, halogen,—CX₃, —CN, —SO₂Cl, —SO_(n)R¹, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸,—NHC═(O)NHNH₂, —NHC═(O)NR′R⁸, —N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹,—C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰, —NR⁷C═(O)R⁹, —NR′C(O)—OR⁹, —NR OR⁹,—OCX₃, —OCHX₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; Twoadjacent R³ substituents may optionally be joined to form a substitutedor unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl. Two R³ substituents bonded to the same atommay optionally be joined to form a substituted or unsubstitutedcycloalkyl or substituted or unsubstituted heterocycloalkyl; R⁷, R⁸, R⁹,and R¹⁰ are independently hydrogen,

halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R⁷ and R⁸ substituents bonded to the samenitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; m and v are independently 1 or 2; n is independently aninteger from 0 to 4; X is independently —Cl, —Br, —I, or —F.

9. The compound of embodiment 1, wherein R¹ is unsubstituted pyridinyl,unsubstituted pyrimidinyl, unsubstituted thiophenyl, unsubstitutedfuranyl, unsubstituted indolyl, unsubstituted benzoxadiazolyl,unsubstituted benzodioxolyl, unsubstituted benzodioxanyl, unsubstitutedthianaphthanyl, unsubstituted pyrrolopyridinyl, unsubstituted indazolyl,unsubstituted quinolinyl, unsubstituted quinoxalinyl, unsubstitutedpyridopyrazinyl, unsubstituted quinazolinonyl, unsubstitutedbenzoisoxazolyl, unsubstituted imidazopyridinyl, unsubstitutedbenzofuranyl, unsubstituted benzothiophenyl, unsubstituted phenyl,unsubstituted naphthyl, unsubstituted biphenyl, unsubstituted pyrrolyl,unsubstituted pyrazolyl, unsubstituted imidazolyl, unsubstitutedpyrazinyl, unsubstituted oxazolyl, unsubstituted isoxazolyl,unsubstituted thiazolyl, unsubstituted furylthienyl, unsubstitutedpyridyl, unsubstituted pyrimidyl, unsubstituted benzothiazolyl,unsubstituted purinyl, unsubstituted benzimidazolyl, unsubstitutedisoquinolyl, unsubstituted thiadiazolyl, unsubstituted oxadiazolyl,unsubstituted pyrrolyl, unsubstituted diazolyl, unsubstituted triazolyl,unsubstituted tetrazolyl, unsubstituted benzothiadiazolyl, unsubstitutedisothiazolyl, unsubstituted pyrazolopyrimidinyl, unsubstitutedpyrrolopyrimidinyl, unsubstituted benzotriazolyl, or unsubstitutedquinolyl.

10. The compound of any one of embodiments 1 to 9, wherein L¹, L² and L³are independently a bond, —NR^(2C)—, —O—, —S—, —C(O)—, —S(O)—, —S(O)₂—,substituted or unsubstituted alkylene, substituted or unsubstitutedheteroalkylene, substituted or unsubstituted cycloalkylene, substitutedor unsubstituted heterocycloalkylene, substituted or unsubstitutedarylene, substituted or unsubstituted heteroarylene; or a substituted orunsubstituted spirocyclic linker; R^(2C) is independently hydrogen, oxo,halogen, —CX^(c) ₃, —CN, —SO₂Cl, —SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c),—NHNH₂, —ONR^(7c)R^(8c), —NHC═(O)NHNH₂, —NHC═(O)NR^(7c)CR^(8c),—N(O)_(m3), —NR^(7c)R^(8c), —C(O)R^(9c), —C(O)—OR^(9c),—C(O)NR^(7c)R^(8c), —OR^(10c), —NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c),—NR^(7c)C(O)—OR^(9c), —NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; Two adjacent R^(2C)substituents may optionally be joined to form a substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; Two R^(2C) substituents bonded to the same atom mayoptionally be joined to form a substituted or unsubstituted cycloalkylor substituted or unsubstituted heterocycloalkyl; R^(7c), R^(8c), R^(9c)and R^(10c) are independently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R^(7c)and R^(8c) substituents bonded to the same nitrogen atom may optionallybe joined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; m1, m3, v1, and v3 areindependently an integer from 1 to 2; n1 and n3 are independently aninteger from 0 to 4; X^(c) is independently —Cl, —Br, —I, or —F.

11. The compound of any one of embodiments 1 to 9, wherein L¹, L² and L³are independently —CR^(2A)R^(2B)—,

R^(2A) and R^(2B) are independently hydrogen, oxo, halogen, —CX^(a) ₃,—CN, —SO₂Cl, —SO_(n1)R^(10a), —SO_(v1)NR^(7a)R^(8a), —NHNH₂,—ONR^(7a)R^(8a), —NHC═(O)NHNH₂, —NHC═(O)NR^(7a)R^(10a), —N(O)_(m1),—NR^(7a)R^(8a), —C(O)R^(9a), —C(O)—OR^(9a), —C(O)NR^(7a)R^(8a),—OR^(1a), —NR^(7a)SO₂R^(10a), —NR^(7a)C═(O)R^(9a), —NR^(7a)C(O)—OR^(9a),—NR^(7a)OR^(9a), —OCX^(a) ₃, —OCHX^(a) ₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(2A) and R^(2B) substituent bonded to the same atom mayoptionally be joined to form a substituted or unsubstituted cycloalkylor substituted or unsubstituted heterocycloalkyl; R^(2C) isindependently hydrogen, oxo, halogen, —CX^(C3), —CN, —SO₂Cl,—SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c), —NHNH₂, —ONR^(7c)R^(8c),—NHC═(O)NHNH₂, —NHC═(O)NR^(7a)CR^(8a), —N(O)_(m3), —NR^(7c)R^(8c),—C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c), —OR^(10c),—NR^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c), —NR^(7c)C(O)—OR^(9c),—NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(7a), R^(8a), R^(9a) and R^(10a) are independentlyhydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R^(7a) and R^(8a) substituents bonded to thesame nitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; R^(7c), R^(8c), R^(9c) and R^(10c) are independentlyhydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH,—SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substitutedor unsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R^(7c) and R^(8c) substituents bonded to thesame nitrogen atom may optionally be joined to form a substituted orunsubstituted heterocycloalkyl or substituted or unsubstitutedheteroaryl; z is independently an integer from 0 to 10; m1, m3, v1, andv3 are independently an integer from 1 to 2; n1 and n3 are independentlyan integer from 0 to 4; X^(a) and X^(c) are independently —Cl, —Br, —I,or —F.

12. The compound of embodiment 10, wherein L¹ is independentlysubstituted or unsubstituted cycloalkylene, substituted or unsubstitutedheterocycloalkylene, substituted or unsubstituted arylene, substitutedor unsubstituted heteroarylene, or substituted or unsubstitutedspirocyclic linker; or L² is independently substituted or unsubstitutedcycloalkylene, substituted or unsubstituted heterocycloalkylene,substituted or unsubstituted arylene, substituted or unsubstitutedheteroarylene, or substituted or unsubstituted spirocyclic linker; or L³is independently substituted or unsubstituted cycloalkylene, substitutedor unsubstituted heterocycloalkylene, substituted or unsubstitutedarylene, substituted or unsubstituted heteroarylene, or substituted orunsubstituted spirocyclic linker.

13. The compound of embodiment 10, wherein L¹ is independentlyR^(2C)-substituted or unsubstituted cycloalkylene, R^(2C)-substituted orunsubstituted heterocycloalkylene, R^(2C)-substituted or unsubstitutedarylene, R^(2C)-substituted or unsubstituted heteroarylene, orR^(2C)-substituted or unsubstituted spirocyclic linker; or L² isindependently R^(2C)-substituted or unsubstituted cycloalkylene,R^(2C)-substituted or unsubstituted heterocycloalkylene,R^(2C)-substituted or unsubstituted arylene, R^(2C)-substituted orunsubstituted heteroarylene, or R^(2C)-substituted or unsubstitutedspirocyclic linker; or L³ is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C)-substituted or unsubstituted heteroarylene, or R^(2C)-substitutedor unsubstituted spirocyclic linker.

14. The compound of embodiment 10, wherein L¹ is independently

or L² is independently

or L³ is independently

and wherein, f2 is independently an integer from 0 to 2; f6 isindependently an integer from 0 to 6; f7 is independently an integerfrom 0 to 7; f8 is independently an integer from 0 to 8; f9 isindependently an integer from 0 to 9; f10 is independently an integerfrom 0 to 10; f12 is independently an integer from 0 to 12; f14 isindependently an integer from 0 to 14.

15. The compound of any one of embodiments 1 to 14, wherein E comprises

R¹³ is independently hydrogen, oxo, halogen, —CX^(b) ₃, —CN, —SO₂Cl,—SO_(r)R¹⁷, —SO_(p)NR¹⁴R¹⁵, —NHNH₂, —ONR¹⁴R¹⁵, —NHC═(O)NHNH₂,—NHC(O)NR¹⁴R¹⁵, —N(O)_(q), —NR¹⁴R¹⁵, —C(O)R¹⁶, —C(O)—OR¹⁶, —C(O)NR¹⁴R¹⁵,—OR¹⁷, —NR¹⁴SO₂R¹⁷, —NR¹⁴C═(O)R¹⁶, —NR¹⁴C(O)—R¹⁶, —NR¹⁴OR¹⁶, —OCX^(b) ₃,—OCHX^(b) ₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; Twoadjacent R¹³ substituents may optionally be joined to form a substitutedor unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; Two R¹³ substituents bonded to the same atommay optionally be joined to form a substituted or unsubstitutedcycloalkyl or substituted or unsubstituted heterocycloalkyl; R¹⁴, R¹⁵,R¹⁶, and R¹⁷ are independently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂,—COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂,—NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH,—OCF₃, —OCHF₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R¹⁴ andR¹⁵ substituents bonded to the same nitrogen atom may optionally bejoined to form a substituted or unsubstituted heterocycloalkyl orsubstituted or unsubstituted heteroaryl; p is independently 1 or 2; q isindependently an integer from 1 to 2; r is independently an integer from0 to 4; X^(b) is independently —Cl, —Br, —I, or —F.

16. The compound of any one of embodiments 1 to 14, wherein E comprisesa substituted or unsubstituted vinyl sulfone moiety, substituted orunsubstituted vinyl sulfonamide moiety, substituted or unsubstitutedfluoro(C₁-C₄)alkylketone moiety, substituted or unsubstitutedchloro(C₁-C₄)alkylketone moiety, substituted or unsubstituted acrylamidemoiety, substituted or unsubstituted disulfide moiety, substituted orunsubstituted thiol moiety, substituted or unsubstituted phosphonatemoiety, substituted or unsubstituted aldehyde moiety, substituted orunsubstituted enone moiety, substituted or unsubstituteddiazomethylketone moiety, substituted or unsubstituted diazomethylamidemoiety, substituted or unsubstituted cyanocyclopropyl carboxamidemoiety, substituted or unsubstituted epoxide moiety, substituted orunsubstituted epoxyketone moiety, substituted or unsubstitutedepoxyamide moiety, substituted or unsubstituted aryl aldehyde moiety,substituted or unsubstituted aryl dialdehyde moiety, substituted orunsubstituted dialdehyde moiety, substituted or unsubstituted nitrogenmustard moiety, substituted or unsubstituted propargyl moiety,substituted or unsubstituted propargylamide moiety.

17. The compound of any one of embodiments 1 to 14, wherein E comprisesan unsubstituted vinyl sulfone moiety, unsubstituted vinyl sulfonamidemoiety, unsubstituted fluoro(C₁-C₄)alkylketone moiety, unsubstitutedchloro(C₁-C₄)alkylketone moiety, unsubstituted acrylamide moiety,unsubstituted disulfide moiety, unsubstituted thiol moiety,unsubstituted phosphonate moiety, unsubstituted aldehyde moiety,unsubstituted enone moiety, unsubstituted diazomethylketone moiety,unsubstituted diazomethylamide moiety, unsubstituted cyanocyclopropylcarboxamide moiety, unsubstituted epoxide moiety, unsubstitutedepoxyketone moiety, unsubstituted epoxyamide moiety, unsubstituted arylaldehyde moiety, unsubstituted aryl dialdehyde moiety, unsubstituteddialdehyde moiety, unsubstituted nitrogen mustard moiety, unsubstitutedpropargyl moiety, or unsubstituted propargylamide moiety.

18. A pharmaceutical composition comprising a pharmaceuticallyacceptable excipient and a compound of any one of embodiments 1 to 17.

19. A method of treating a disease in a patient in need of suchtreatment, said method comprising administering a therapeuticallyeffective amount of a compound of any one of embodiments 1 to 17 to said patient.

20. The method of embodiment 19, wherein said disease is cancer.

21. The method of embodiment 20, wherein said cancer is colon cancer,colorectal cancer, pancreatic cancer, breast cancer, or leukemia.

22. The method of embodiment 20, wherein said cancer is lung cancer.

23. The method of embodiment 22, wherein said lung cancer is non-smallcell lung cancer.

24. A method of modulating the activity of a K-Ras protein, said methodcomprising contacting said K-Ras protein with an effective amount of acompound of any one of embodiments 1 to 17.

25. The method of embodiment 24, wherein said modulating of saidactivity comprises modulating GTPase activity, nucleotide exchange,differential GDP or GTP binding, effector protein binding, effectorprotein activation, guanine exchange factor (GEF) binding,GEF-facilitated nucleotide exchange, phosphate release, nucleotiderelease, nucleotide binding, K-Ras subcellular localization, K-Raspost-translational processing, or K-Ras post-translationalmodifications.

26. The method of embodiment 24, wherein said modulating is increasingthe activity of said K-Ras protein.

27. The method of embodiment 24, wherein said modulating is reducing theactivity of said K-Ras protein.

28. The method of embodiment 24, wherein said K-Ras protein is a humanK-Ras protein.

29. The method of embodiment 28, wherein said human K-Ras proteincontains a G12C, G12D, G13C, or G13D mutation.

30. The method of embodiment 28, wherein said human K-Ras proteincontains a G12C mutation.

31. A method of modulating a K-Ras protein, said method comprisingcontacting said K-Ras protein with an effective amount of a compound ofany one of embodiments 1 to 17.

32. The method of embodiment 31, wherein said modulating is of K-Rassubcellular localization, K-Ras post-translational processing, or aK-Ras post-translational modification.

33. The method of embodiment 31, wherein said K-Ras protein is a humanK-Ras protein.

34. The method of embodiment 33, wherein said human K-Ras proteincontains a G12C, G12D, G13C, or G13D mutation.

35. The method of embodiment 33, wherein said human K-Ras proteincontains a G12C mutation.

36. The method of any one of embodiments 24 to 35, wherein said K-Rasprotein is within a biological cell.

37. The method of embodiment 36, wherein said biological cell forms partof an organism.

38. A K-Ras protein covalently bound to a compound of any one ofembodiments 1 to 17, wherein said compound is covalently bound to acysteine residue of said K-Ras protein.

39. The covalently modified K-Ras protein of embodiment 38, wherein saidcompound is reversibly covalently bound to a cysteine residue of saidK-Ras protein.

40. The covalently modified K-Ras protein of embodiment 38, wherein saidcompound is irreversibly covalently bound to a cysteine residue of saidK-Ras protein.

41. The covalently modified K-Ras protein of any one of embodiments 38to 40, wherein said covalently modified K-Ras protein has a modulatedactivity relative to a control, wherein said activity is selected fromGTPase activity, nucleotide exchange, differential GDP or GTP binding,effector protein binding, effector protein activation, guanine exchangefactor (GEF) binding, GEF-facilitated nucleotide exchange, phosphaterelease, nucleotide release, nucleotide binding, K-Ras subcellularlocalization, K-Ras post-translational processing, and K-Raspost-translational modifications.

42. The covalently modified K-Ras protein of any one of embodiments 38to 40, wherein said covalently modified K-Ras protein is modulated inK-Ras subcellular localization, K-Ras post-translational processing, orK-Ras post-translational modification.

43. The covalently modified K-Ras protein of any one of embodiments 38to 40, wherein said K-Ras protein contains a G12C mutation.

44. The covalently modified K-Ras protein of embodiment 43, wherein saidcompound is covalently bonded to cysteine residue 12.

45. The covalently modified K-Ras protein of any one of embodiments 38to 40, wherein said K-Ras protein contains a G13C mutation.

46. The covalently modified K-Ras protein of embodiment 45, wherein saidcompound is covalently bonded to cysteine residue 13.

47. A K-Ras protein covalently bound to a compound of any one ofembodiments 1 to 17, wherein said compound is covalently bound to anaspartate residue of said K-Ras protein.

48. The covalently modified K-Ras protein of embodiment 47, wherein saidcompound is reversibly covalently bound to an aspartate residue of saidK-Ras protein.

49. The covalently modified K-Ras protein of embodiment 47, wherein saidcompound is irreversibly covalently bound to an aspartate residue ofsaid K-Ras protein.

50. The covalently modified K-Ras protein of any one of embodiments 47to 49, wherein said covalently modified K-Ras protein has a modulatedactivity relative to a control, wherein said activity is selected fromGTPase activity, nucleotide exchange, differential GDP or GTP binding,effector protein binding, effector protein activation, guanine exchangefactor (GEF) binding, GEF-facilitated nucleotide exchange, phosphaterelease, nucleotide release, nucleotide binding, K-Ras subcellularlocalization, K-Ras post-translational processing, and K-Raspost-translational modifications.

51. The covalently modified K-Ras protein of any one of embodiments 47to 49, wherein said covalently modified K-Ras protein is modulated inK-Ras subcellular localization, K-Ras post-translational processing, orK-Ras post-translational modification.

52. The covalently modified K-Ras protein of any one of embodiments 47to 49, wherein said K-Ras protein contains a G12D mutation.

53. The covalently modified K-Ras protein of embodiment 52, wherein saidcompound is covalently bonded aspartate residue 12.

54. The covalently modified K-Ras protein of any one of embodiments 47to 49, wherein said K-Ras protein contains a G13D mutation.

55. The covalently modified K-Ras protein of embodiment 54, wherein saidcompound is covalently bonded to aspartate residue 13.

56. A method of identifying a covalent inhibitor of K-Ras proteincomprising: contacting a K-Ras protein with a K-Ras inhibitor testcompound; allowing said K-Ras inhibitor test compound to covalentlyinhibit said K-Ras protein; detecting the level of covalent inhibitionof said K-Ras protein thereby identifying a covalent inhibitor of K-Rasprotein.

57. The method of embodiment 56, wherein said K-Ras inhibitor testcompound is a Switch 2—Binding Pocket covalent inhibitor test compoundand said K-Ras protein is a G12C mutant K-Ras protein.

58. The method of embodiment 57 further comprising the steps of:contacting a wildtype K-Ras protein with said Switch 2—Binding Pocketcovalent inhibitor test compound; allowing said Switch 2—Binding Pocketcovalent inhibitor test compound to inhibit said wildtype K-Ras protein;detecting the level of inhibition of said wildtype K-Ras protein;comparing the level of inhibition of said wildtype K-Ras protein to thelevel of covalent inhibition of said G12C mutant K-Ras protein, whereina higher level of covalent inhibition of said G12C mutant K-Rasindicates said Switch 2—Binding Pocket covalent inhibitor test compoundis specific for said G12C mutant K-Ras protein.

59. The method of embodiment 56, wherein said K-Ras inhibitor testcompound is a Switch 2—Binding Pocket covalent inhibitor test compoundand said K-Ras protein is a G12D mutant K-Ras protein.

60. The method of embodiment 59 further comprising the steps of:contacting a wildtype K-Ras protein with said Switch 2—Binding Pocketcovalent inhibitor test compound; allowing said Switch 2—Binding Pocketcovalent inhibitor test compound to inhibit said wildtype K-Ras protein;detecting the level of inhibition of said wildtype K-Ras protein;comparing the level of inhibition of said wildtype K-Ras protein to thelevel of covalent inhibition of said G12D mutant K-Ras protein, whereina higher level of covalent inhibition of said G12D mutant K-Rasindicates said Switch 2—Binding Pocket covalent inhibitor test compoundis specific for said G12D mutant K-Ras protein.

61. The method of embodiment 56, wherein said K-Ras inhibitor testcompound is a Switch 2—Binding Pocket covalent inhibitor test compoundand said K-Ras protein is a G13C mutant K-Ras protein.

62. The method of embodiment 61 further comprising the steps of:contacting a wildtype K-Ras protein with said Switch 2—Binding Pocketcovalent inhibitor test compound; allowing said Switch 2—Binding Pocketcovalent inhibitor test compound to inhibit said wildtype K-Ras protein;detecting the level of inhibition of said wildtype K-Ras protein;comparing the level of inhibition of said wildtype K-Ras protein to thelevel of covalent inhibition of said G13C mutant K-Ras protein, whereina higher level of covalent inhibition of said G13C mutant K-Rasindicates said Switch 2—Binding Pocket covalent inhibitor test compoundis specific for said G13C mutant K-Ras protein.

63. The method of embodiment 56, wherein said K-Ras inhibitor testcompound is a Switch 2—Binding Pocket covalent inhibitor test compoundand said K-Ras protein is a G13D mutant K-Ras protein.

64. The method of embodiment 59 further comprising the steps of:contacting a wildtype K-Ras protein with said Switch 2—Binding Pocketcovalent inhibitor test compound; allowing said Switch 2—Binding Pocketcovalent inhibitor test compound to inhibit said wildtype K-Ras protein;detecting the level of inhibition of said wildtype K-Ras protein;comparing the level of inhibition of said wildtype K-Ras protein to thelevel of covalent inhibition of said G13D mutant K-Ras protein, whereina higher level of covalent inhibition of said G13D mutant K-Rasindicates said Switch 2—Binding Pocket covalent inhibitor test compoundis specific for said G13D mutant K-Ras protein.

65. A method of selectively modulating a Ras protein, said methodcomprising contacting said Ras protein with a compound which contacts atleast one amino acid residue forming a Switch 2 binding pocket of saidRas protein, wherein said at least one amino acid residue is selectedfrom valine-7, valine-9, glycine-10, proline-34, threonine-58,glycine-60, glutamine-61, glutamate-62, glutamate-63, arginine-68,tyrosine-71, methionine-72, tyrosine-96, glutamine-99 and isoleucine-100of said Ras protein, and wherein said compound covalently reacts with anamino acid residue of said Ras protein.

66. The method of embodiment 65, wherein said compound binds to a K-Rasprotein with a higher binding affinity as compared to a H-Ras protein.

67. The method of embodiment 65, wherein said compound interacts with atleast one of glycine-60, glutamate-62, or glutamate-63.

68. The method of embodiment 65, wherein said interacting between saidamino acid residue and said compound involves hydrogen bonding, van derWaals interaction, ionic bonding, covalent bonding, or hydrophobicinteraction.

69. The method of embodiment 65, wherein said compound fills spacewithin said Switch 2 binding pocket.

70. The method of embodiment 65, wherein said compound inhibits K-Ras asmeasured by the fraction of protein covalently labeled by the compound,wherein the compound is present in 50-fold excess and wherein thefraction of protein covalently labeled is determined by massspectrometry.

71. The method of embodiment 65, wherein said compound covalently reactswith an amino acid residue of said K-ras protein.

72. The method of embodiment 71, wherein said amino acid residue iscysteine-12 of K-Ras G12C mutant protein.

73. A method of designing a compound which covalently binds to a Switch2 binding pocket of a K-Ras protein, the method comprising the steps of:providing a structural model of a reference compound bound to the Switch2 binding pocket of the K-Ras protein, wherein the reference compound isnon-covalently bound to said Switch 2 binding pocket; identifying acysteine, aspartate, lysine, tyrosine or glutamate residue located inproximity to said Switch 2 binding pocket when said reference compoundis bound to said Switch 2 binding pocket; generating at least oneadditional structural model of a test compound bound to said Switch 2binding pocket, wherein said test compound comprises an electrophilicmoiety; and selecting said test compound if said electrophilic moiety islocated within bonding distance of said cysteine residue when said testcompound is bound to said Switch 2 binding pocket.

74. A compound having molecular dimensions compatible with the shape ofa K-Ras Switch 2 binding pocket wherein the compound, when present in anaqueous solution comprising 200 μM of the compound and 4 μM K-Ras,covalently binds to at least 50% of K-Ras proteins present in solutionafter 24 hours.

75. A compound of Formula:

or a pharmaceutically acceptable salt thereof, wherein: e5 is an integerfrom 0 to 5; X′ is —O—, —NH—, or —S—; R^(2A) and R^(2B) areindependently hydrogen, substituted or unsubstituted alkyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; R^(2A)and R^(2B) substituent bonded to the same atom may optionally be joinedto form a substituted or unsubstituted cycloalkyl or substituted orunsubstituted heterocycloalkyl; R³ is independently hydrogen, oxo,halogen, —CX₃, —CN, —SO₂Cl, —SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸,—NHC═(O)NHNH₂, —NHC═(O)NR⁷R⁸, —N(O)_(m), —NR′R⁸, —C(O)R⁹, —C(O)—OR⁹,—C(O)NR⁷R⁸, —OR¹⁰, —NR⁷SO₂R¹⁰, —NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹,—OCX₃, —OCHX₂, substituted or unsubstituted alkyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted heterocycloalkyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; L² isindependently R^(2C)-substituted or unsubstituted cycloalkylene,R^(2C)-substituted or unsubstituted heterocycloalkylene,R^(2C)-substituted or unsubstituted arylene, R^(2C)-substituted orunsubstituted heteroarylene, or R^(2C)-substituted or unsubstitutedspirocyclic linker; L³ is independently R^(2C)-substituted orunsubstituted cycloalkylene, R^(2C)-substituted or unsubstitutedheterocycloalkylene, R^(2C)-substituted or unsubstituted arylene,R^(2C)-substituted or unsubstituted heteroarylene, or R^(2C)-substitutedor unsubstituted spirocyclic linker; E is an electrophilic chemicalmoiety capable of forming a covalent bond with a cysteine or aspartateresidue; R^(2C) is independently hydrogen, oxo, halogen, —CX^(c) ₃, —CN,—SO₂Cl, —SO_(n3)R^(10c), —SO_(v3)NR^(7c)R^(8c), —NHNH₂, —ONR^(7c)R^(8c),—NHC═(O)NHNH₂, —NHC═(O)NR^(7c)R^(8c), —N(O)_(m3), —NR^(7c)R^(8c),—C(O)R^(9c), —C(O)—OR^(9c), —C(O)NR^(7c)R^(8c), —OR^(10c),—N^(7c)SO₂R^(10c), —NR^(7c)C═(O)R^(9c), —NR^(7c)C(O)—OR^(9c),—NR^(7c)OR^(9c), —OCX^(c) ₃, —OCHX^(c) ₂, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; two adjacent R^(2C) substituents may optionally be joined toform a substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; two R^(2C) substituents bondedto the same atom may optionally be joined to form a substituted orunsubstituted cycloalkyl or substituted or unsubstitutedheterocycloalkyl; R⁷, R⁸, R⁹, and R¹⁰ are independently hydrogen,halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₂Cl, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂, —NHC═(O) NH₂, —NHSO₂H,—NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedheterocycloalkyl, substituted or unsubstituted aryl, or substituted orunsubstituted heteroaryl; R^(7a), R^(8a), R^(9a) and R^(10a) areindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R^(7a) and R^(8a) substituentsbonded to the same nitrogen atom may optionally be joined to form asubstituted or unsubstituted heterocycloalkyl or substituted orunsubstituted heteroaryl; R^(7c), R^(8c), R^(9c) and R^(10c) areindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O) NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; m, m1, m3, v, v1, and v3 areindependently 1 or 2; n, n1, and n3 are independently an integer from 0to 4; X, X^(a) and X^(c) are independently —Cl, —Br, —I, or —F.

76. The compound of embodiment 75, wherein E comprises a substituted orunsubstituted vinyl sulfone moiety, substituted or unsubstituted vinylsulfonamide moiety, substituted or unsubstituted peroxide moiety,substituted or unsubstituted fluoro(C₁-C₄)alkylketone moiety,substituted or unsubstituted chloro(C₁-C₄)alkylketone moiety,substituted or unsubstituted acrylamide moiety, substituted orunsubstituted disulfide moiety, substituted or unsubstituted thiolmoiety, substituted or unsubstituted phosphonate moiety, substituted orunsubstituted aldehyde moiety, substituted or unsubstituted enonemoiety, substituted or unsubstituted diazomethylketone moiety,substituted or unsubstituted diazomethylamide moiety, substituted orunsubstituted cyanocyclopropyl carboxamide moiety, substituted orunsubstituted epoxide moiety, substituted or unsubstituted epoxyketonemoiety, substituted or unsubstituted epoxyamide moiety, substituted orunsubstituted aryl aldehyde moiety, substituted or unsubstituted aryldialdehyde moiety, substituted or unsubstituted dialdehyde moiety,substituted or unsubstituted nitrogen mustard moiety, substituted orunsubstituted propargyl moiety, substituted or unsubstitutedpropargylamide moiety.

77. The compound or pharmaceutically acceptable salt of embodiment 75,wherein L² is independently R^(2C)-substituted or unsubstitutedheterocycloalkylene or R^(2C)-substituted or unsubstituted spirocycliclinker and L³ is a bond.

78. The compound or pharmaceutically acceptable salt of embodiment 75,wherein L² is monocyclic 4, 5, or 6-membered heterocycloalkylene.

79. The compound or pharmaceutically acceptable salt of embodiment 75,wherein L² is unsubstituted piperazino or unsubstituted piperidino.

80. The compound or pharmaceutically acceptable salt of embodiment 75,wherein L² is bicyclic fused heterocycloalkylene.

81. The compound or pharmaceutically acceptable salt of embodiment 75,wherein L² is an unsubstituted spirocyclic linker.

82. The compound or pharmaceutically acceptable salt of embodiment 75,wherein E is a substituted or unsubstituted vinyl sulfone moiety,substituted or unsubstituted vinyl sulfonamide moiety, or a substitutedor unsubstituted acrylamide moiety.

83. The compound or pharmaceutically acceptable salt of embodiment 75,having the formula:

84. A method of treating a disorder in a subject in need thereof,comprising: determining the presence or absence of a K-Ras mutation in amalignant or neoplastic cell isolated from the subject; and if a K-Rasmutation is determined to be present in the subject, administering tothe subject a therapeutically effective amount of a compound orpharmaceutically acceptable salt of any one of embodiments 1-17 and74-83.

85. A method of treating a disorder in a subject in need thereof,comprising: determining the presence or absence of a K-Ras mutation in amalignant or neoplastic cell isolated from the subject, in connectionwith the prescription of an effective amount of a compound orpharmaceutically acceptable salt of any one of embodiments 1-17 and74-83 to said subject; and if a K-Ras mutation is determined to bepresent in the subject, providing an alert to a caregiver of saidsubject.

86. The method of embodiment 84 or 85, wherein the disorder is cancer.

87. A method of treating cancer in a human subject in need thereof,comprising administering to said subject at least one compound orpharmaceutically acceptable salt of any one of embodiments 1-17 and74-83, wherein said subject has a K-Ras mutation.

88. The method of any one of embodiments 84 to 87, wherein the K-Rasmutation is selected from the group consisting of G12C, G13C, G12D, andG13D.

89. The method of embodiment 88, wherein the K-Ras mutation is G12C.

90. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound modulates thebinding of GDP or GTP to a K-Ras protein.

91. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound inhibits thebinding of GDP or GTP to a K-Ras protein.

92. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound increases thebinding of GDP or GTP to a K-Ras protein.

93. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound inhibits thebinding of GTP to a K-Ras protein.

94. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound increases thebinding of GDP to a K-Ras protein.

95. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound inhibits therelease of GDP from a K-Ras protein.

96. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound increases therelease of GDP or GTP from a K-Ras protein.

97. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound increases therelease of GDP from a K-Ras protein.

98. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound increases therelease of GTP from a K-Ras protein.

99. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound modulates thebinding of a K-Ras protein to Raf.

100. The compound, or a pharmaceutically acceptable salt thereof, of anyone of embodiments 1-17 and 74-83, wherein said compound inhibits thebinding of a K-Ras protein to Raf.

101. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound modulates the binding of GDP or GTP to a K-Rasprotein.

102. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound inhibits the binding of GDP or GTP to a K-Rasprotein.

103. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound increases the binding of GDP or GTP to a K-Rasprotein.

104. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound inhibits the binding of GTP to a K-Ras protein.

105. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound increases the binding of GDP to a K-Ras protein.

106. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound inhibits the release of GDP from a K-Ras protein.

107. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound increases the release of GDP or GTP from a K-Rasprotein.

108. The method of any one of embodiments 19-37, 65-72, and 84-89, wherein said compound increases the release of GDP from a K-Ras protein.

109. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound increases the release of GTP from a K-Ras protein.

110. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound modulates the binding of a K-Ras protein to Raf.

111. The method of any one of embodiments 19-37, 65-72, and 84-89,wherein said compound inhibits the binding of a K-Ras protein to Raf.

112. The method of any one of embodiments 19-37, 65-72, 84-89, and101-111, wherein said compound binds a GDP bound K-Ras protein.

113. The compound of any one of embodiments 1-17, 74-83, and 90-100,wherein said compound binds a GDP bound K-Ras protein.

114. A pharmaceutical composition comprising a pharmaceuticallyacceptable excipient and a compound of any one of embodiments 74-83,90-100, and 113.

EXAMPLES

The following examples are meant to illustrate certain embodiments ofthe invention and not to limit the scope of the invention describedherein. Activating mutations in K-Ras are among the most common lesionsfound in human cancer, and such mutations are generally associated withpoor prognosis. Despite numerous efforts in academia and industry, smallmolecule inhibitors that directly target K-Ras remain elusive. Even morehighly desired are molecules that selectively target mutant K-Ras whilesparing the wild type protein. We have used a fragment-based screen todiscover oncogenic mutant-specific inhibitors of K-Ras. Crystallographicstudies with multiple inhibitors in complex with K-Ras reveal that thecompounds bind in a novel hydrophobic pocket that is not apparent in anypublished crystal structure of Ras. These inhibitors disrupt theconformations of Switch I and Switch II, domains that are essential forthe association and activation of downstream signaling partners. Ourmedicinal chemistry effort has greatly improved potency, showing thatthis pocket is particularly amenable to chemical optimization. In vitrobiochemical characterization of these inhibitors confirms that theyblock Ras function. Our discovery of a new druggable pocket in K-Ras,and a set of inhibitors that bind to it in a mutant-specific fashion,provides a promising new avenue for the direct pharmacologicalinhibition of oncogenic Ras. In embodiments, inhibitors bind to anallosteric pocket behind Switch II, selectively bind to GDP-bound stateand not to GTP-bound state, the structure of inhibitor-Ras complexsuggests potential to block formation of proper GTP-bound conformationand impair effector activation, and/or inhibitors slow GEF-catalyzednucleotide exchange, suggesting they might trap Ras in the inactivestate.

Compound Binding to K-Ras

In some embodiments, compounds described herein are divided into threedistinct parts: a terminal portion (e.g. R¹ above), a linker portion(e.g. L1-L2-L3-above) and a chemically reactive portion (e.g. E above).In some embodiments, the terminal portion is a hydrophobic moiety andmay comprise a phenyl ring. In some further embodiments the hydrophobicmoiety is substituted with at least one halogen atom. In someembodiments the linker portion is a flexible linker portion. The linkerportion may include a substituted or unsubstituted saturatedheterocycloalkylene. In some embodiments, the chemically reactiveportion forms a covalent bond with a thiol of the oncogenic G12C mutantof K-Ras.

In some embodiments of the compounds described herein, the hydrophobicterminal portion (e.g. R¹) binds the K-Ras protein in a deep pocket thatis not apparent in structures of the protein without a compound. In someembodiments, the deep pocket is formed by compound binding. As shown inligand interaction maps (FIGS. 7 and 8), this binding pocket includesthe following amino acids: valine-7, valine-9, threonine-58,arginine-68, tyrosine-71, methionine-72, tyrosine-96. In someembodiments of the compounds, having a hydrophobic terminal portion, thepocket may form a hydrophobic counterpart to the compounds. In someembodiments, several of the interacting amino acids (e.g. residuescontacting a compound) are integral parts of Switch-2, a flexible regionof K-Ras involved in effector binding and downstream signaling. In someembodiments of K-Ras bound to a compound as disclosed herein, Switch 2looks distinct from the active conformation of Switch 2 in GTP-boundK-Ras. In some embodiments, the changes in Switch-2 upon compoundbinding may be how the compounds described herein (includingembodiments) modulate K-Ras, K-Ras activity, and/or K-Ras function (e.g.decreasing the binding affinity of compound bound K-Ras for a signalingpathway interacting protein (e.g. PI3K)).

In some embodiments, the linker portion of compounds described herein(e.g. L¹, L², and L³) shows interactions with the K-Ras protein. In someembodiments of the compounds described herein, the linker portion ismore solvent exposed than the terminal portion. In some embodiments, thelinker portion of the compounds described herein contacts amino acidresidues of Switch-2. In some embodiments, a Switch 2 residue contactedby the linker portion is glycine-60, glutamate-62 or glutamate-63. Insome embodiments, the linker portion contacts all three residues. Insome embodiments, contact between the compound linker portion and K-Rasprovides stabilization of the unusual protein conformation that may beinduced by compound binding. In some embodiments of the compoundsdescribed herein, the linker portion of the compounds described hereinhave flexibility in regard to chemical composition, while stillproviding modulation of K-Ras.

In some embodiments of the compounds, several groups have been found tobe effective as the reactive portion of the compounds (e.g. E, theelectrophilic moiety, thiol reactive, aspartate reactive). In someembodiments, the compounds are disulfide based compounds to link thecompound to K-Ras cysteine-12. X-ray crystal structures (e.g.JO-01-189cbut) show clear electron density for the disulfide linkage.Due to the possible instability of disulfide linkages in the reducingenvironment of cells we developed compounds with different reactiveportions (e.g. electrophilic moieties) that can covalently (e.g.reversibly, irreversibly) bind to cysteine and aspartate. In someembodiments, the electrophilic moiety E is selected from vinyl sulfones,acrylamides and epoxides. In some embodiments, crystal structures forcompounds containing the electrophilic moiety vinyl sulfone showinteractions of the sulfone oxygens with either the protein directly orwith ordered water molecules. In some embodiments of the compounds,compounds containing sulfones are sterically more demanding thandisulfide containing compounds. In some embodiments, the electrophilicmoiety E (e.g. vinyl sulfones) can modulate the conformation ofSwitch-1. In some embodiments, the modulation of Switch 1 by compoundbinding may modulate K-Ras activity or function (e.g. effector binding,for example Raf or PI3K). In some embodiments, the compound binding toK-Ras may modulate K-Ras metal binding by modulating Switch 1 structureor function (e.g. partially disordering Switch-1 relative to the Switch1 conformation in K-Ras that is not bound to a compound as describedherein). In some embodiments, the electrophilic group E contributes tothe binding of compound to K-Ras by contacting K-Ras residues. In someembodiments, the electrophilic group E contributes to the binding ofcompound to K-Ras by covalently bonding to K-Ras through a cysteine oraspartate at residues 12 or 13. The right balance between chemicallyreactivity, sterical demands and favorable interactions with the proteinneeds to be achieved for the best reactive group to link the compound tooncogenic cysteine-12.

In some embodiments, the compounds described herein (includingembodiments, examples and compounds of Table 1, 2, 3, 4, or 5) provideinteractions with K-Ras through a novel complementary pocket and theterminal portion including R¹, that leads to a previously unknownconformation of Switch-2, and a covalent link of the compound to theoncogenic mutant K-Ras (e.g. G12C, G12D, G13C, G13D), through thereactive portion containing E. In some embodiments, E can contribute toK-Ras binding through interactions beyond the covalent bond formationand can modulate Switch-1 conformation and stability. In someembodiments, by utilizing both features with the described compounds,K-Ras G12C or G12D or G13C or G13D can be selectively targeted.

Structure-Activity Relationships of Compound Examples

In some embodiments, where the the terminal portion includes a phenyl(e.g. R¹ includes a phenyl ring), a hydrophobic group is preferred inthe 2-position on the phenyl ring, ortho to the O, S, or N linking tothe rest of the molecule (e.g. L¹, L², or L³). In some embodiments, theterminal portion includes a phenyl substituted with a larger halogen. Insome embodiments, R¹ is a phenyl substituted with a substituted orunsubstituted aryl or substituted or unsubstituted heteroaryl at theortho position to the bond to the linker portion. In some embodiments,R¹ is a phenyl substituted with a substituted or unsubstituted fusedring aryl or substituted or unsubstituted fused ring heteroaryl at theortho position to the bond to the linker portion. In some embodiments,these hydrophobic substituents (e.g. substituted or unsubstituted arylor substituted or unsubstituted heteroaryl) on R¹ (e.g. phenyl ring)ortho to the bond to the linker portion, point toward the same affinitypocket in K-Ras. In some embodiments, bulky substituents are welltolerated at the 5-position of phenyl relative to the bond to the linkerportion. In some embodiments, this position may accommodate bulky groupssuch as a propargyl group, without compromising affinity. In someembodiments, the 6 position on an R¹ phenyl group (relative to the orthoat the 2 position described previously in this paragraph) is anon-hydrophobic group. In some embodiments, the terminal portionincludes a fused ring such as a fused ring aryl or fused ringheteroaryl.

In some embodiments of the compounds, the linker portion is bonded tothe S2BP moiety through a secondary amine. In some embodiments of thecompounds linker portion is bonded to the S2BP moiety through an etheror thioether. In some embodiments, the linker portion is not a rigidmoiety. In some embodiments, the linker includes a ring (e.g.substituted or unsubstituted heterocycloalkylene, substituted orunsubstituted cycloalkylene, substituted or unsubstituted arylene.substituted or unsubstituted heteroarylene substituted or unsubstitutedfused rings, substituted or unsubstituted spirocyclic rings). In someembodiments, the linker portion includes a diamine. In some embodimentsthe linker portion positions the S2BP binding moiety R¹ and theelectrophilic moiety E for optimal contact with the S2BP and a cysteineor asparate respectively.

In some embodiments, the electrophilic moiety E may have flexibility. Insome embodiments, optimization of the electrophile positioning and angleof attack may provide compounds with greater binding and potency.

The Switch 2—Binding Pocket

In some embodiments, the S2BP binding moiety or S2BP binding compoundinteract with one or more of amino acid residues V7, V9, G10, P34, T58,G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and 1100 of K-Ras or theequivalent (i.e. corresponding) amino acids present in mutants orhomologs of K-Ras. In some embodiments, the S2BP binding moiety or S2BPbinding compound displace one or more amino acids in Switch 2 of K-Rasthat interact, in the GTP bound form, with one or more of the aminoacids of the Switch 2 Binding Region of K-Ras, or the equivalent (i.e.corresponding) amino acids present in mutants or homologs of K-Ras. Insome embodiments, the S2BP binding moiety or S2BP binding compounddisplace one or more amino acids in the Switch 2 Binding Region of K-Rasthat interact, in the GTP bound form, with one or more of the Switch 2residues of K-Ras, or the equivalent (i.e. corresponding) amino acidspresent in mutants or homologs of K-Ras.

In some embodiments, the Switch 2—Binding Pocket binding moietyadditionally interacts (e.g. bonds) with an amino acid that forms partof the Switch 2—Binding Pocket. In some related embodiments, theinteraction is a hydrogen bond, van der Waals interaction, ionic bond,covalent bond (e.g. disulfide bond) or hydrophobic interaction.

Switch 2—Binding Pocket Binding Moieties that Interact with the Switch2—Binding Pocket

In some embodiments, to determine whether the Switch 2—Binding Pocketbinding moiety or Switch 2—Binding Pocket binding compound contactsand/or fills space within the Switch 2—Binding Pocket, computer modelingtechniques are employed. In some embodiments, a query Switch 2—BindingPocket binding compound (i.e. a test or reference compound) is fit intoa structural model, such as a computer image, of Ras (e.g. K-Ras). Insome embodiments, the structural model is derived from one or more ofthe solved co-crystal structures of human K-Ras bound to a compound asdescribed herein. The PyMOL Molecular Graphics System may be employed togenerate the image. Examples are presented in FIG. 7 or 8, wherein twocompounds are built into the computer image of K-Ras, derived from theirrespective co-crystal structures with K-Ras.

The computer models are typically analyzed to prevent any gross stericclashes and to satisfy key hydrogen bonds between the query Switch2—Binding Pocket binding compound and the K-Ras protein. In someembodiments, energy minimization calculations are performed to optimizebinding energy. Using these techniques, one skilled in the art caneasily determine whether a query Switch 2—Binding Pocket bindingcompound includes a Switch 2—Binding Pocket binding moiety that fillsspace within the Switch 2—Binding Pocket.

In some embodiments, the query Switch 2—Binding Pocket binding compoundis analyzed to determine whether at least one bond (e.g. a hydrogenbond) is formed between the query Switch 2—Binding Pocket bindingcompound and an amino acid that forms part of the Switch 2—BindingPocket. In some embodiments, using a computer modeling technique asdescribed above, the distance between one or more amino acids that formpart of the Switch 2—Binding Pocket and a potential contact point on theSwitch 2—Binding Pocket binding moiety is determined. In someembodiments, based on this distance, one skilled in the art maydetermine whether at least one bond is formed between one or more aminoacids that form part of the Switch 2—Binding Pocket and a Switch2—Binding Pocket binding moiety.

Identification of Covalent K-Ras Inhibitors

The invention further provides a method of designing a compound whichcovalently binds to a Switch 2 binding pocket of a K-Ras protein, themethod comprising the steps of: a) providing a structural model of areference compound bound to the Switch 2 binding pocket of the K-Rasprotein, wherein the reference compound is covalently or non-covalentlybound to said Switch 2 binding pocket; b) identifying a cysteine,aspartate, lysine, tyrosine or glutamate residue located in proximity tosaid Switch 2 binding pocket when said reference compound is bound tosaid Switch 2 binding pocket; c) generating at least one additionalstructural model of a test compound bound to said Switch 2 bindingpocket, wherein said test compound comprises an electrophilic moiety;and d) selecting said test compound if said electrophilic moiety islocated within bonding distance of said cysteine, aspartate, lysine,tyrosine or glutamate residue when said test compound is bound to saidSwitch 2 binding pocket.

A structural model of a reference compound bound to a Switch 2 bindingpocket of a Ras protein (such as K-Ras, N-Ras, or H-Ras) may be providedas described above. Any suitable structural model of a referencecompound bound covalently or non-covalently to the Ras protein can beused. For example, a three-dimensional computer model or arepresentation thereof (e.g. a computer image) is used. In someembodiments, an X-Ray crystal structure is used. For example, one of thesolved co-crystal structures of human K-Ras can be used. In someembodiments, a structural model of a Switch 2 binding pocket of a K-Rasprotein is used. Structural models can be obtained from publicdatabases, including but not limited to the RCSB Protein Data Bank,available online at pdb.org and rcsb.orb. Alternatively, structuralmodels can also be obtained and manipulated by computer modeling,including homology modeling and folding studies.

Suitable reactive amino acid residues can be identified by analyzing thesequence of the protein in conjunction with the structural model towhich the reference compound is bound. Putative reactive amino acidresidues which are cysteine, aspartate, lysine, tyrosine or glutamatemay be identified in proximity to the reference compound. For example,cysteine residues in proximity to the reference compound are identified.Once an amino acid residue in the structural model has been identified,the intermolecular distance between the reference compound and theputative reactive amino acid may be noted. In some embodiments, thedistance between the putative reactive amino acid and at least one atomof the reactive compound is less than or equal to 15, 12, 10, 8, 6, or 4angstroms.

Test compounds comprising an electrophilic moiety may subsequently usedto generate additional structural models in which the position of theelectrophilic moiety relative to one or more of the identified putativereactive amino acid residues is noted. The bonding distance between thetest compound and one of such residues may be calculated based on thestructural model, and a determination may be made regarding thepotential bonding distance between the test compound (e.g. theelectrophilic moiety) and the putative reactive residue. Test compoundswhich appear to provide a suitable bonding distance likely to result inthe formation of a covalent bond may then be chosen for furtherdevelopment. When making such determinations, factors such as sterichindrance and orientation of each chemical moiety may be taken intoaccount. Test compounds which are initially rejected may also be furthermodified in order to improve the likelihood that they will form acovalent bond with the target protein.

In some embodiments, the compounds described herein target a mutant ofK-Ras, glycine-12 to cysteine (G12C). This is the most common Rasmutation in lung cancer (Forbes et al. 2006 Br J Cancer) and the onlyknown transforming mutation found in a recent comparative sequencingstudy of a human lung tumor (Lee et al. 2010 Nature). 100% of K-Rasmutations in MYH-associated polyposis (familial colon cancer syndrome)are K-RasG12C (Jones, S., Lambert, S., Williams, G. T., Best, J. M.,Sampson, J. R., & Cheadle, J. P. (2004). Increased frequency of thek-ras G12C mutation in MYH polyposis colorectal adenomas. BritishJournal of Cancer, 90(8), 1591-1593. doi:10.1038/sj.bjc.6601747) G12Cplaces a nucleophilic sulfhydryl group between the nucleotide-bindingsite and the allosteric site. Since the regions surrounding both sitesare involved in interactions with effectors and GEFs, binding ofcompounds (e.g. antagonists, inhibitors, small molecules) at either sitehas the potential to disrupt downstream signaling. In some embodiments,the location and nucleophilicity of this mutant residue allowsdevelopment of covalent (e.g. reversible, irreversible) inhibitors ofoncogenic K-Ras that bind in either the active site or the cleft behindSwitch 2 or the Switch 2—Binding Pocket.

In some embodiments, a library of disulfide compounds may be screenedagainst a cysteine-containing protein in the presence of a reducingagent such as β-mercaptoethanol (BME). Compounds with complementarybinding interactions with a region of the protein near the cysteine mayshift the disulfide exchange equilibrium away from BME modification ofthe cysteine thiol and enhance the ratio of the hit ligand bound to thecysteine (see FIG. 3). The resulting mass change of the protein can bereadily detected by mass spectrometry, and the percentage of modifiedprotein can be used as a measure of potency. Compounds which exchangewith the cysteine without conferring affinity should exchange withreducing agent equally well and will not shift the equilibrium towardprotein modification. The potency of various compounds at a givenconcentration of BME may be compared by calculating the dose-response 50(DR50), which is the concentration of compound at which the proteinbecomes 50% modified.

In some embodiments, screening is for inhibitors of K-Ras G12C, anaturally occurring, oncogenic form of the target does not requireremoval of the mutant cysteine residue.

The crystal structure of the complex between H-Ras and SOS (Margarit etal. 2003 Cell) shows that a deep nucleotide pocket has been pried open,and the interface between Ras and SOS creates two new clefts on eitherside of Ras residue 12.

The Switch 1 and Switch 2 areas of Ras show significant structuraldifferences between the GDP- and GTP-bound states. Moreover, theseregions are involved in interactions with all known Ras bindingpartners, including effectors, GEFs and GAPs (See FIG. 1). In someembodiments, the compounds described herein covalently modifycysteine-12 thereby altering the conformation of either switch regionaffecting GEF binding or effector protein binding. Multiple modes ofcompound (e.g. small molecule, antagonist, inhibitor) interruption ofRas function can be employed.

In some embodiments, the compounds provided herein effect the Rasbinding to Raf or PI3K. In some embodiments, binding of the compoundsprovided herein to K-Ras modulates K-Ras binding to Raf. In someembodiments, binding of the compounds provided herein to K-Ras modulatesK-Ras binding to PI3K. In some embodiments, binding of the compoundsprovided herein to K-Ras modulates K-Ras binding to PI3K but not K-Rasbinding to Raf. In some embodiments, binding of the compounds providedherein to K-Ras reduces K-Ras binding to PI3K but not K-Ras binding toRaf. In some embodiments, binding of the compounds provided herein toK-Ras modulates K-Ras binding to Raf but not K-Ras binding to PI3K. Insome embodiments, binding of the compounds provided herein to K-Rasreduces K-Ras binding to Raf but not K-Ras binding to PI3K. In otherembodiments, the compounds provided herein alter intrinsic orGEF-enhanced nucleotide exchange. In other embodiments, the compoundsprovided herein alter Ras binding to SOS. In other embodiments, thecompounds provided herein modulate SOS-enhanced nucleotide exchange. Insome embodiments, the compounds provided herein increase the intrinsicor GAP-stimulated rate of GTP hydrolysis. In some embodiments, thecompounds provided herein decrease the intrinsic affinity of K-Ras fornucleotide. In some embodiments, the compounds provided herein decreasethe intrinsic affinity of K-Ras for GTP. In some embodiments, thecompounds provided herein decrease the intrinsic affinity of K-Ras forGDP.

Residue 12 of K-Ras lies between the nucleotide-binding site and anallosteric pocket. In some embodiments, the compounds provided hereinbind to either site or both sites. In some embodiments, compound bindingto the allosteric pocket alters K-Ras-effector interactions. In someembodiments, compound binding to the S2BP alters K-Ras-effectorinteractions. In some embodiments, compound binding to thenucleotide-binding site alters K-Ras-effector interactions. In someembodiments, simultaneous compound binding to the allosteric pocket andthe nucleotide-binding site alters K-Ras-effector interactions. In someembodiments, simultaneous compound binding to the S2BP and thenucleotide-binding site alters K-Ras-effector interactions. In someembodiments, compound binding to the allosteric pocket, S2BP, and/ornucleotide-binding site alters the activity of the K-Ras protein, it'sGTPase activity, nucleotide exchange, effector protein binding, effectorprotein activation, guanine exchange factor (GEF) binding,GEF-facilitated nucleotide exchange, phosphate release, nucleotiderelease, nucleotide binding, K-Ras subcellular localization, K-Raspost-translational processing, K-Ras post-translational modifications,or GTP bound K-Ras signaling pathway.

In some embodiments, the compounds described herein afford a covalentyet reversible handle.

Determining Intrinsic and GEF mediated nucleotide exchange rates forcompound-bound K-RasG12C

GEF-mediated nucleotide exchange assays were carried out usingfull-length recombinant human K-Ras G12C and WT containing an N-terminalhexahistidine tag and the catalytic domain of SOS (residues 566-1049),also containing a hexahistidine tag, in the presence of α-³²P-labeledGTP. K-Ras WT and G12C were treated with 250 μM inhibitor overnight at 4C in the following buffer: 20 mM HEPES [pH 7.5], 150 mM NaCl, 10 mMEDTA. The percent modification was determined by mass spectrometry(Waters Acquity TQD). The proteins were then run over NAP-5 columns,eluting with Buffer A (20 mM HEPES [pH 7.5], 150 mM NaCl, 20 mM MgCl₂),following the manufacturer's instructions. Reaction mixes were preparedcontaining 4 μM K-Ras and 1 μM SOS in Buffer A with 1 mg/mL BSA.Separately, a solution of [α-³²P] GTP (160 pCi/mL, 2 μM total GTP) wasprepared. The reactions were initiated by adding 25 μL GTP solution to25 μL of each reaction mixture. Exchange was measured by blotting thereaction onto nitrocellulose, washing with Buffer A, then visualizing byphosphorimager.

Recombinant Protein Expression of K-Ras

Hexahistidine-tagged recombinant human K-Ras (isoform 2, residues 1-169,based on construct used for pdb entry 3GFT) was transformed intoEscherichia coli (BL21 (DE)). After the bacterial growth to an OD(600)of 0.4-0.6 in Terrific Broth containing 30 mg/L kanamycin at 37 C,induction was carried out at 18 C using 0.5 mM IPTG and growth wascontinued at 18° C. for about 18h. The bacteria were harvested bycentrifugation and the obtained pellet either stored at −80 C or usedfreshly for the subsequent steps.

The pellet was resuspended in lysis buffer (500 mM NaCl, 20 mM TRISpH=8, 5 mM imidazole) containing protease inhibitor cocktail (Rochecomplete EDTA free), the bacteria were lysed by microfluidizer, 2 mM BME(final) was added and cell debris was removed by ultracentrifugation.The supernatant was incubated for 1 h with Co-affinity beads (Clontech,˜2 mL bed volume per 1 L initial culture), the loaded beads then washedwith lysis buffer containing 2 mM BME and the protein eluded with buffercontaining 125-250 mM imidazole. The hexahistidine tag was then cleavedusing Hexahistidine-tagged TEV-protease (1 mg recombinant TEV per 25 mgcrude K-Ras, 1 mg GDP added per 20 mg crude K-Ras) while dialyzingagainst a buffer containing 300 mM NaCl, 20 mM TRIS pH=8, 5 mMimidazole, 1 mM DTT, 0.5 mM EDTA. The cleaved protein was then diluted5-fold with low salt buffer (50 mM NaCl, 20 mM TRIS pH=8), incubatedwith Ni-agarose beads (Qiagen) to remove uncleaved protein and protease,and 5 mM MgCl2 and GDP was added to fully load the metal and nucleotidesite of K-Ras.

The crude protein was then purified by ion exchange chromatography(HiTrap Q HP column, salt gradient from 50 to 500 mM NaCl) to give thepartially purified protein, commonly in following buffer (˜230 mM NaCl,20 mM TRIS pH=8, small amounts of GDP).

At this point the partially purified protein was either fully labeledwith the desired compound (incubation overnight with an excess ofcompound at 4 C, labeling checked by massspec analysis), frozen down andstored at −80 C, or used for further purification.

The last purification step for the labeled or unlabeled protein wasgel-filtration using a Superdex 200 column (10/300 GL) with thefollowing buffer: 20 mM HEPES pH=7.5, 150 mM NaCl and 1 mM DTT (for theunlabeled proteins). The freshly prepared and purified protein was thenconcentrated to 5-20 mg/mL and used for the X-ray crystallography trays.

X-Ray Crystallography

Sequences for the different K-Ras constructs were generallycodon-optimized and synthesized by DNA2.0 using the pJexpress411 vector.For the X-ray structures of compound labeled K-Ras G12C a specialcysteine-light mutant was used (G12C, C51 S, C80L, C118S) to enable moreuniformly labeled species.

For X-ray crystallography 1 mM magnesium chloride and 40 microM GDP(final) were added to the freshly purified protein. After high speedcentrifugation hanging drop crystallization conditions were set up bymixing 1:1 protein and precipitation solutions. Common successfulreservoir conditions were: 28-32% PEG3000, 200 mM NaCl, 100 mM TrispH=7; 1.8-2.2M 2:3 NaH2PO4:K2HPO4, 0.1M NaAc; 28-32% PEG4000, 200 mMNH4CH3COO, 100 mM Na-citrate pH=5.6; 18-22% PEG8000, 100 mM CaCl2, 100mM Tris pH=7.5; 18-22% PEG3350, 0.2M CaCl2, pH=7.5. After a varyingamount of time, commonly several days, at 20 C three dimensionalcrystals were observed. If necessary crystals were cryoprotected in thecrystallization solution supplemented with glycerol, flash frozen andstored in liquid nitrogen prior to obtaining diffraction data atbeamlines 8.2.1/8.2.2 (100 K nitrogen stream) at the Berkeley LabAdvanced Light Source. Data was initially processed with HKL2000 (HKLResearch, Inc., scaling) and then solved by molecular replacement andrefined to the indicated statistics using Phoenix (Adams et al.).

Mass Spectrometric Screen for Extent of Covalent Labeling

Un-tagged recombinant K-Ras G12C (1-169) at 4 μM in Buffer A was reactedwith inhibitors at 200 μM or 10 μM (2% DMSO final). At 2, 6, and 24 hrs,10 μL aliquots were removed and the reactions were stopped by additionof 1 μL 2% formic acid. The extent of modification was determined bymass spectrometry.

Disulfide Library Screen

We screened a library of disulfide compounds for covalent modificationof K-RasG12C (1-169) as determined by mass spectrometry. Hit compoundswill be defined as those causing >50% modification of Ras at aconcentration of 100 μM while in the presence of 100 μM BME. It has beenshown previously that EDTA increases the nucleotide exchange rate ofboth H-Ras (Hattori et al. 1987 Mol Cell Biol) and K-Ras (Hara et al.1988 Oncogene Res). The EDTA chelates Mg²⁺ and destabilizes thenucleotide bound state of Ras. To enhance the possibility of findingmolecules which bind to the GTP site. The screen was carried out in thepresence of EDTA. Once hits have been identified, compound titrationswill be carried out in the presence of 200 μM BME to determine theirDR50. These compounds will also be counter-screened against wild-typeK-Ras to verify that they modify the mutant cysteine and not one of thethree cysteines already present in the wild-type sequence. Whiletreatment of Ras with EDTA increases the rate of nucleotide exchange bytwo orders of magnitude, nucleotide exchange factors can increase therate by a factor of 10⁵. With a higher rate of exchange, we may be morelikely to identify compounds binding in the GTP site.

We have screened a library of 480 tethering compounds at 100 μM eachagainst K-RasG12C (1-169) in the presence of 100 μM BME and 10 mM EDTA.From this screen we have identified 17 molecules which reach >50%modification of Ras. A disulfide containing hit (6H05) reached 95%modification, and titration experiments gave a DR50 of 31 μM. None ofour hit compounds from this library screen caused greater than 10%modification of wild-type K-Ras, suggesting they are specificallytethering to the mutant cysteine. When the entire library was screenedagainst H-RasG12C only 6H05 exhibited greater than 50% modification (seeFIG. 5).

All disulfide hit compounds identified in this screen were less potentin the absence of EDTA, including 6H05. However, when GDP andnon-hydrolyzable GTP (GMPPNP) were each titrated up to 0.8 mM in thepresence of EDTA, there was no detectable effect on modification. Thisresult strongly suggests that 6H05 does not share a binding site withnucleotide.

To begin understanding the structure-activity relationship of 6H05, wedesigned and synthesized a family of 10 analogues (see FIG. 6). One ofthese analogues, JO-148A, showed slightly increased potency over 6H05with a DR50 of 27 μM in the presence of EDTA. In addition, this analogueretained a DR50 of 63 μM in the presence of 10 mM MgCl₂ and 100 μMGMPPNP. Under these conditions, over the course of the experimentessentially no nucleotide exchange is expected to occur.

Determining Intrinsic GTPase and GAP Mediated Activity of Compound-BoundK-Ras G12C

The assays will be carried out as described previously (Schubbert etal., Mol. Cell Biol. 2007, 7765-70). 200 nM of each recombinant K-Rasprotein (G12C, compound loaded G12C, G12D, WT) that had been preloadedwith [γ-³²P]GTP is incubated without (intrinsic GTPase activity assay)or with (GAP assays) GAP-related domain (GRD) proteins (neurofibromin orp120 GAP) at room temperature. The hydrolyzed and released radioactivephosphate is extracted and detected by liquid scintillation counting atdefined time points. Recombinant K-Ras and GRD proteins are produced inEscherichia coli.

Determining Occupancy of the Pocket by Click Chemistry

Lysate from Calu-1 (G12C), NCI H-1792 (G12C), or HEK cells is treatedwith 10 μM inhibitor or DMSO for 24 hrs at 4° C. Ras is thenimmunoprecipitated with anti-Ras antibody on magnetic beads. ImmobilizedRas is then treated with 200 μM Ras-069 (propargyl) for 24 hrs at 4 C.Rhodamine-azide or biotin-azide is then attached to the propargyl groupof Ras-069 by Cu-catalyzed click reaction. Following elution of theproteins, the extent of modification by Ras-069 is visualized by Westernblot (biotin) or fluorescence imager (rhodamine), and reveals the extentof K-RasG12C with an unoccupied allosteric pocket after inhibitortreatment. Thus, the extent of inhibitor modification is anti-correlatedwith Western or fluorescence signal.

Initial Stop Flow Experiments

Conditions: 1 micM protein, buffer: 20 mM HEPES pH=7.5, 150 mM NaCl, 1mM DTT, 2 mM unlabeled GDP if indicated, 1 micM SOS if indicated, 2.5 mMEDTA if indicated, no added free Mg in buffer, protein loaded withmant-dGDP, (1 h r.t. incubation with 2 mM EDTA, NAP-5 purification),protein pre-labeled with compounds and frozen, experiment at 20 C.Results:fast intrinsic bleaching/exchange, larger drop in fluorescencedue to EDTA treatment with compound, acceleration of exchange inpresence of SOS.

Continued Stop Flow Experiments

Conditions:1 micM protein (same), buffer (changed): 40 mM HEPES pH=7.5,10 mM MgCl2, 1 mM DTT, 0.1 mM unlabeled GDP if indicated (changed), 0.1mM unlabeled GTP if indicated (new), 1 micM SOS if indicated (sameconcentration), 15 mM EDTA if indicated (changed), now contains free Mgin buffer (s.a.), protein loaded with mant-dGDP. (1 h r.t. incubationwith 2 mM EDTA, NAP-5 purification), protein pre-labeled with compoundsand frozen, experiment at 20 C. Results: lowered intrinsic exchange,less effect of EDTA, initial drop (may need more?), basically no SOSacceleration. Ongoing experiments comparing GDP vs. GTP.

Crystallization Screen

Carried out screen for ˜500 conditions with labeled protein loaded witheither nucleotide. Found large number (>10 conditions) that showedcrystallization with either form, more for GDP, some overlap inconditions. Followed up on conditions: 9 for GDP, 6 for GppNp (same forall 3 compounds). Reproduced fairly well (about ½ of conditions)

Compound Binding Perturbs Nucleotide Binding (GTP Vs. GDP)

More than 15 co-crystal structures confirm novel pocket behind Switch IIwith strong SAR. Inhibitors block nucleotide exchange and decrease Rafbinding. It is possible to specifically inhibit proliferation ofKrasG12C-driven cancer cell lines by treating under serum deprivation.Experiments being conducted to obtain more complete signaling data,including for control compound. FIGS. 12, 13, and 15 to 19 showmodulation of K-ras conformation by compound binding, which modulatesnucleotide binding site (e.g. GTP binding) and show novel bindingpocket.

Compound Binding to K-Ras Alters Affinities for GTP and GppNp (GNP),(See FIGS. 34 to 36 and Tables 6 to 8)

The corresponding recombinantly expressed, full-length K-Ras protein(wild type, G12C-mutant, G12C-mutant labeled fully with either compound055 (Ras-055) or 083 (Ras-083)) at about 10 micM (micromolar)concentration was incubated with 200 micM mant-d-GDP in the presence of2.5 M EDTA. After one hour at room temperature MgCl₂ to a finalconcentration of 10 mM was added. The protein was then run through aNAP-5 column to remove free nucleotide. The concentration of theobtained protein was determined by Bradford assay and the protein wasthen used in the described plate-based assay. For the assay 10 micL ofthe prepared protein in reaction buffer (20 mM HEPES pH=7.5, 150 mMNaCl, 1 mM DTT, 1 mM MgCl₂) was added to a well of a low volume blackbottom plate (Corning, #3676). The fluorescence intensity was measuredon a spectramax M5 plate reader (Molecular devices, 360 nm excitation,440 nm emission) to provide a value used in later normalization. Then 5micL of an EDTA solution with the indicated nucleotide (GDP, GTP, orGppNp) was added to each well and the reaction mix was allowed toequilibrate for two hours at room temperature. Measurement of thefluorescent intensity at this time provided the end point. Samples weremeasured in duplicates for each experiment. In the final mix theconcentrations were the following: protein (1 micM), EDTA (5 mM),nucleotide (as indicated, titrated in 2.5-fold dilution series,15-points). Curves show results from one representative experiment, thecolumn-graph shows the averaged data from three experiments withstandard deviation shown as error. For the determination of IC50 foreach nucleotide a sigmoidal curve fit was used (Prism-software).

Compound binding to K-Ras reduces SOS-mediated exchange (dissociation ofmant-d-GDP monitored). The corresponding recombinantly expressed,full-length K-Ras protein (wild type, G12C-mutant, G12C-mutant labeledfully with either compound 055 or 083) at about 10 micM concentrationwas incubated with 200 micM mant-d-GDP in the presence of 2.5 M EDTA.After one hour at room temperature MgCl₂ to a final concentration of 10mM was added. The protein was then run through a NAP-5 column to removefree nucleotide. The concentration of the obtained protein wasdetermined by Bradford assay and the protein was then used in thedescribed plate-based assay. Concentration of recombinantly expressedSOS-protein was determined by Bradford assay as well. For the assay 10micL of the prepared protein in reaction buffer (20 mM HEPES pH=7.5, 150mM NaCl, 1 mM DTT, 1 mM MgCl₂) was added to a well of a low volume blackbottom plate (Corning, #3676). Then 5 micL of either buffer (forintrinsic rate), SOS-solution, or EDTA-solution containing the indicatednucleotide (GDP, GTP, or GppNp) was added to each well. The fluorescenceintensity of each reaction was followed on a spectramax M5 plate reader(Molecular devices, 360 nm excitation, 440 nm emission) over five hours(18000 seconds) at one minute intervals. Samples were measured intriplicate for each experiment. In the final mix the concentrations werethe following: protein (1 micM), EDTA (if present: 5 mM), SOS (ifpresent: 1 micM), nucleotide (as indicated: ˜200 micM, excess). Curvesshow results from one representative experiment, the table shows theaveraged data from three experiments with standard deviation shown aserror. For the determination of half-lives a one-phase exponential decaymodel was used (Prism-software).

Compound binding to K-Ras reduces SOS-mediated exchange (association ofmant-d-GDP or mant-d-GppNp monitored). Protein concentrations of freshlythawed, recombinantly expressed, GDP-loaded full-length K-Ras protein(wild type, G12C-mutant, G12C-mutant labeled fully with either compound055 or 083) and SOS were determined by Bradford assay. Then a K-Rassolution containing varying amount of SOS in reaction buffer (20 mMHEPES pH=7.5, 150 mM NaCl, 1 mM DTT, 1 mM MgCl₂) was prepared and 10micL were added to each well of a low volume black bottom plate(Corning, #3676). The exchange reaction was started by addition ofeither 5 micL of a mant-d-GDP or mant-d-GppNp solution in reactionbuffer. The fluorescence intensity of each reaction was followed on aspectramax M5 plate reader (Molecular devices, 360 nm excitation, 440 nmemission) over five hours (18000 seconds) at one minute intervals.Samples were measured in triplicate for each experiment. In the finalmix the concentrations were the following: K-Ras (1 micM), SOS (0(intrinsic), 0.25-4 micM, 2-fold dilution series),mant-d-GDP/mant-d-GppNp (1 micM). Curves show results from onerepresentative experiment, the table shows the averaged data from threeexperiments with standard deviation shown as error. For thedetermination of half-lives a one-phase association model was used(Prism software).

TABLE 1 Obtained structures (Electrophiles) ordered by increasingpotency: Labeling percentage + <=5%, 5% < ++ <=20%, 20%< +++ <=40%, 40%< ++++ <=60%, 60% < +++++ Labeling % Resolution/ (10 micM) Space groupR-free/ Structure Compound 24h Unit cell R-work JO-02- 112D

+++ (plate) 3 sets 1.35A 1.35A 1.40A C121 (75,40,55A) (90,105,90)0.1806/ 0.1504 0.1809/ 0.1577 0.1937/ 0.1537 JO-02-172

+ (plate) 2.09 A C121 (71,83,87A) (90,109,90) Diff. orient. 0.2285/0.1897 JO-02-31A

++ (plate) 1.70 A C121 (68,83,85A) (90,111,90) 0.2106/ 0.1763 JO-02-56A

++++ (plate) 2.30 A P22121 (93,108, 121A) (90,90,90) 0.2218/ 0.1809Ras-028

+++ (plate) 1.55 A C121 (68,84,86A) (90,111,90) 0.1966/ 0.1814 Ras-055(C2)

+++++ (plate) 1.57 A C121 (68,84,87A) (90,111,90) 0.1931/ 0.1584 Ras-055(P1)

+++++ (plate) 1.49 A P1 (33,40,62A) (77,82,78) 0.2122/ 0.1752 Ras-059

+++++ (single) 1.58A C121 (68,84,87A) (90,111,90) 0.1913/ 0.1740 Ras-062

+++ (single) 1.94A C121 (68,84,87A) (90,111,90) 0.2351/ 0.1948 UP-I-177C

++++ (plate) 1.57 A C121 (68,84,86A) (90,111,90) 0.2087/ 0.1837UP-I-185a

+++++ (single) 1.81A C121 (68,84,87A) (90,111,90) 0.2038/ 0.1801

TABLE 2 Obtained structures (Disulfides) ordered by increasing potency:Labeling percentage + <=5 micromolar, 5 micromolar < ++ <=20 micromolar,20 micromolar < +++ <=40 micromolar, 40 micromolar < ++++ <=60micromolar, 60 micromolar < +++++ Resolution/ Potency/ Space groupR-free/ Structure Compound Labeling Unit cell R-work JO-01-148

++++ (EC50 at 200 micM BME) Tethering 1.50 A P1 (33,39,63A) (77,81,77)0.1977/ 0.1639 JO-01-189 Cbut

++ (EC50 at 200 micM BME) Tethering 1.29 A P1 (33,39,62A) (78,82,78)0.1723/ 0.1591

TABLE 3 Eletrophilic K-Ras Modulators (e.g. covalent S2BP bindingcompounds). Percent reduction in activity of compound at 10 micromolarrelative to control (no compound): + <=5%, 5% < ++ <=20%, 20% < +++ <=40%, 40% < ++++ <= 60%, 60% < +++++. Structure Name Mol Weight 2 hrs 6hrs 24 hrs

Ras-001 396.268 + + +

Ras-002 391.677 + + +

Ras-003 312.366 + + +

Ras-004 312.366 + + +

Ras-005 326.393 + + +

Ras-006 326.393 + + +

Ras-007 414.326 + + +

Ras-008 427.73 + + +

Ras-009 348.42 + + +

Ras-010 362.447 + + +

Ras-011 461.283 + + +++

Ras-012 362.447 + + +

Ras-013 418.295 + + ++

Ras-014 348.42 + + +

Ras-015 437.736 + + +++

Ras-016 415.892 + + +

Ras-017 376.831 + + +

Ras-018 372.867 + + +++

Ras-019 408.3 + + ++

Ras-020 416.876 + + +

Ras-021 383.85 + + +

Ras-022 450.337 + + +

Ras-023 401.865 + + +

Ras-024 422.327 + + +

Ras-025 429.918 + + +

Ras-026 436.353 + + ++

Ras-027 452.353 + + +

Ras-028 392.301 + + +++

Ras-029 427.945 + + +

Ras-030 484.737 + + ++++

Ras-031 429.918 + + +

Ras-032 387.882 + + +

Ras-033 373.855 + + +

Ras-034 401.908 + + +

Ras-035 436.31 + + +

Ras-036 519.182 + ++ ++++

Ras-037 451.321 + + ++

Ras-038 437.295 + + +

Ras-039 409.285 + + ++

Ras-040 472.181 + + +++

Ras-041 388.866 + + ++

Ras-042 386.85 + + ++

Ras-043 435.322 + + +

Ras-044 437.338 + + ++

Ras-045 461.323 + + +

Ras-046 575.098 + + +

Ras-047 472.364 + + +

Ras-048 453.337 + + ++

Ras-049 480.363 + + +

Ras-050 423.311 + + ++

Ras-051 388.866 + + ++

Ras-052 532.224 + + ++

Ras-053 519.182 + ++ ++++

Ras-054 422.327 + +++ +++++

Ras-055 408.3 ++ +++ +++++

Ras-056 459.347 + + +

Ras-057 920.597 + ++ ++++

JO-01-171 357.232 + + +

JO-01-172 343.205 + + +

JO-02-26 409.351 + + ++

JO-02-31A 393.285 + + ++

JO-02-31B 388.933 + + ++

JO-02-31C 424.965 + + +++

JO-02-31D 409.351 + + +

JO-02-36A 353.222 + + +

JO-02-36B 367.248 + + +

JO-02-37A 317.168 + + +

JO-02-37B 331.194 + + +

JO-02-38B 255.317 + + +

JO-02-49A 367.85 + + +

JO-02-49B 351.396 + + +

JO-02-49C 363.431 + + +

JO-02-74A 405.296 + + +++

JO-02-74B 419.323 + + ++

JO-02-74C 405.296 + + ++

JO-02-72 373.231 + + +

JO-02-77A 359.248 + + +

JO-02-55 393.285 + + ++

JO-02-56A 450.337 + + ++++

JO-02-56B 450.337 + + ++

JO-02-112A 419.323 + + ++

JO-02-112B 433.349 + + ++

JO-02-112C 407.312 + + +

JO-02-112D 379.259 + + +++

JO-02-115A 358.84 + + +

JO-02-115B 407.312 + + +

JO-02-115C 407.312 + + +

JO-02-115D 427.73 + + +++

JO-02-116A 441.757 + + +

JO-02-116B 428.719 + + +

JO-02-125 312.368 + + +++

JO-02-139E 340.785 + + +

JO-02-144 518.197 + ++ +++++

JO-02-152 498.143 + + +++

UP-I-162B 508.416 + + +

UP-I-164A 362.491 + + +

UP-I-164B 346.426 + + +

UP-I-164C 345.441 + + +

UP-I-165B 460.332 + + +

UP-I-165C 366.396 + + +

UP-I-165D 361.503 + + +

UP-I-177C 465.348 + ++ ++++

UP-I-177D 554.25 + + +++++

UP-I-177E 648.251 + + +++++

JO-02-155 468.117 + ++ ++++

Ras-058 422.327 + + +

Ras-059 420.354 + ++ +++++

Ras-060 538.23 + + +

Ras-061 486.39 + + +

Ras-062 372.246 + + +++

UP-I-154B 407.55 + + +

UP-I-160B 394.512 + + +

JO-02-157A (R) 468.117 + + +

JO-02-157B (S) 468.117 + + ++

Ras-063 409.285 + ++ +++

Ras-064 417.908 + + +++

Ras-065 455.88 + ++ +++

Ras-066 405.799 + + ++

Ras-067 426.838 + + ++

Ras-068 518.197 + + +

Ras-069 447.333 + ++ +++++

Ras-070 437.338 + + +++

Ras-071 417.307 + + ++++

Ras-072 538.23 + + +

UP-I-185a 450.363 ++ +++ +++++

UP-I-185b 408.3 + + ++

UP-I-187 434.298 + + +++

UP-I-154A 444.332 + + +

UP-I-154K 412.55 + + +

Ras-073 +++ +++++

Ras-074 ++++

Ras-075 −

Ras-076 −

Ras-077 ++ +++++

Ras-078 −

JO-02-31A +++

Ras-079 +++ +++++ +++++

Ras-080 +++

Ras-081 +++ ++++ +++++

Ras-082 +++ +++++

Ras-083 +++ +++++

Ras-084 +++ +++++ +++++

Ras-085 ++ +++ +++++

Ras-086 ++++

Ras-087

TABLE 4 Modulation of Ras by compound binding. 12Cα to 60Cα distance (Å)Switch I Metal ion GDP-bound WT 8 Mg Hras G60A 8.1 Mg (1XJ0) JO-02-1728.3 Mg JO-02-112D 8.4 Mg JO-02-56A 8.5 Mg Chain D JO-02-56A 8.6 Mg ChainE JO-01-148 9 Ca JO-01-189 9.1 Ca Ras-055_P1 9.5 Ca (Ras-055 in P1)Ras-028 11.1 disordered — JO-02-56A 11.2 disordered Mg Chain C JO-02-31A11.6 disordered — JO-02-56A 11.7 disordered — Chain A Ras-055_C2 11.9disordered — (Ras-055 in C2) UP-I-185a 12 disordered — Ras-059 12.6disordered — UP-I-177C 12.8 disordered — JO-02-56A no density disordered— Chain B Ras-062 no density disordered — GTP-bound Hras G12C 3.8 MgKras WT state 3.9 Mg state 2 (3GFT) Rap1A 3.9 Mg (RafRBD) (1C1Y) HrasT35S state 3.9 Mg 2 (2KKM) Hras T35S state 4.9 low affinity state Mg 1(3KKN) Kras WT state 1 4.9 low affinity state Mg (4EFL) Hras G60A 5.2low affinity state Mg (1XCM)

TABLE 5 Labeling % Resolution/ (10 micM) Space group R-free/ StructureCompound 24h Unit cell R-work JO-02- 112D

+++ (plate) 3 sets 1.35A 1.35A 1.40A C121 (72,40,55A) (90,105,90)0.1806/ 0.1504 0.1809/ 0.1577 0.1937/ 0.1537 JO-02-172

+ (plate) 2.09 A C121 (71,83,87A) (90,109,90) Diff. orient. 0.2285/0.1897 JO-02-31A

++ (plate) 1.70 A C121 (68,83,85A) (90,111,90) 0.2106/ 0.1763 JO-02-56A

++++ (plate) 2.30 A P22121 (93,108, 121A) (90,90,90) 0.2218/ 0.1809Ras-028

+++ (plate) 1.55 A C121 (68,84,86A) (90,111,90) 0.1966/ 0.1814 Ras-055(C2)

+++++ (plate) 1.57 A C121 (68,84,87A) (90,111,90) 0.1931/ 0.1584 Ras-055(P1)

+++++ (plate) 1.49 A P1 (33,40,62A) (77,82,78) 0.2122/ 0.1752 Ras-059

+++++ (single) 1.58A C121 (68,84,87A) (90,111,90) 0.1913/ 0.1740 Ras-062

+++ (single) 1.94A C121 (68,84,87A) (90,111,90) 0.2351/ 0.1948 UP-I-177C

++++ (plate) 1.57 A C121 (68,84,86A) (90,111,90) 0.2087/ 0.1837UP-I-185a

+++++ (single) 1.81A C121 (68,84,87A) (90,111,90) 0.2038/ 0.1801UP-I-185a (update, delete the old one)

+++++ (single) 1.49A C121 (68,84,86A) (90,111,90) 0.1908/ 0.1689 Ras-069

+++ (single) 1.74A C121 (69,85,87A) (90,111,90) 0.2098/ 0.1849 Ras-079(C2)

+++++ (single) 1.37A C121 (68,84,84A) (90,111,90) 0.1918/ 0.1652 Ras-079(P212121)

+++++ (single) 1.93A P212121 (39,43,88A) (90,90,90) 0.2086/ 0.1736Ras-081

+++++ (single) 2.04A C121 (68,84,86A) (90,110,90) 0.2169/ 0.1836UP-I-177E

++++ (plate) 2.27 A C121 (68,85,86A) (90,111,90) 0.2340/ 0.1857 UP-I-187

+++ (single) 1.59A C121 (68,84,87A) (90,111,90) 0.2004/ 0.1753

TABLE 6 Calculated/estimated half-lives from experiments in FIGS.34A-34B. mant-dGDP Calculated/Estimated Half-lives mant-dGDP intrinsicSOS, 4 μM SOS, 2 μM SOS, 1 μM SOS, 0.5 μM SOS, 0.25 μM WT >18000 s 350 ±40 s 420 ± 40 s 1030 ± 130 s 1850 ± 200 s 4500 ± 800 s G12C >18000 s 580± 70 s 810 ± 80 s 2100 ± 400 s 3700 ± 300 s 10700 ± 3000 sG12C-055 >18000 s 11300 ± 2500 s 10500 ± 4200 s >18000 s >18000 s >18000s G12C-083 >18000 s 8200 ± 2400 s >18000 s >18000 s >18000 s >18000 s

TABLE 7 Calculated/estimated half-lives from experiments in FIGS.35A-35B. mant-dGppNp Calculated/Estimated Half-Lives mant-dGppNpintrinsic SOS, 4 μM SOS, 2 μM SOS, 1 μM SOS, 0.5 μM SOS, 0.25 μMWT >18000 s 610 ± 70 s 940 ± 100 s 2000 ± 150 s 3300 ± 140 s 7000 ± 500s G12C >18000 s 1160 ± 70 s 1780 ± 70 s 3860 ± 730 s 4480 ± 80 s 16300 ±1500 s G12C-055 no reliable data obtained G12C-083 no reliable dataobtained

TABLE 8 Calculated/estimated half-lives from experiments in FIGS.36A-36D. Calculated/Estimated Half-lives SOS/GDP SOS/GTP SOS/GppNpEDTA/GDP EDTA/GTP EDTA/GppNp WT 2080 ± 140 s 1010 ± 50 s 1120 ± 70 s 117± 6 s 112 ± 3 s 107 ± 2 s G12C 3640 ± 340 s 1560 ± 320 s 1640 ± 160 s157 ± 5 s 151 ± 4 s 143 ± 5 s G12C-055 >18000 s >18000 s >18000 s 247 ±14 s 232 ± 13 s 197 ± 10 s G12C-083 >18000 s >18000 s >18000 s 370 ± 7 s334 ± 7 s 304 ± 11 s

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It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

What is claimed is:
 1. A K-Ras protein covalently bonded to a compound,wherein the compound is covalently bonded to cysteine residue 12 of theK-Ras protein and is in contact with one or more amino acid residues ofa K-Ras protein Switch 2 binding pocket.
 2. The K-Ras protein of claim1, wherein the one or more amino acid residues of the K-Ras proteinSwitch 2 binding pocket are selected from the group consisting of V7,V9, G10, K16, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, andI100.
 3. The K-Ras protein of claim 1, wherein the one or more aminoacid residues of the K-Ras protein Switch 2 binding pocket comprise atleast three amino acid residues selected from the group consisting ofV7, V9, G10, K16, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99,and I100.
 4. The K-Ras protein of claim 1, wherein the one or more aminoacid residues of the K-Ras protein Switch 2 binding pocket are selectedfrom the group consisting of K16, R68, M72, Y96, and Q99.
 5. The K-Rasprotein of claim 1, wherein the compound has an electrophilic chemicalmoiety covalently bonded to cysteine residue 12 of the K-Ras protein,wherein the electrophilic chemical moiety is a substituted orunsubstituted acrylamide.
 6. The K-Ras protein of claim 1, wherein thecompound has an electrophilic chemical moiety covalently bonded tocysteine residue 12 of the K-Ras protein, wherein electrophilic chemicalmoiety is:

wherein R¹³ is hydrogen, halogen, —CX^(b) ₃, or —CN; and X^(b) is Cl,Br, I or F.
 7. The K-Ras protein of claim 1, wherein the compound hasthe formula:R¹-L¹-L²-L³-E, wherein: R¹ is a Switch 2 Binding Pocket binding moiety;L¹ is a bond or a divalent radical chemical linker; L² is a bond; L³ is

f8 is an integer from 0 to 8; R^(2C) is independently hydrogen orsubstituted or unsubstituted alkyl; and E is an electrophilic chemicalmoiety covalently bonded with cysteine residue 12 of the K-Ras protein.8. The K-Ras protein of claim 7, wherein E is:

wherein R¹³ is hydrogen, halogen, —CX^(b) ₃, or —CN; and X^(b) is Cl,Br, I or F.
 9. The K-Ras protein of claim 7, wherein: R¹ is R³—substituted or unsubstituted aryl or R³-substituted or unsubstitutedheteroaryl; R³ is independently hydrogen, oxo, halogen, —CX₃, —CN,—SO₂Cl, —SO_(n)R¹⁰, —SO_(v)NR⁷R⁸, —NHNH₂, —ONR⁷R⁸, —NHC═(O)NHNH₂,—NHC═(O)NR⁷R⁸, —N(O)_(m), —NR⁷R⁸, —C(O)R⁹, —C(O)—OR⁹, —C(O)NR⁷R⁸,—NR⁷SO₂R¹⁰, —NR⁷C═(O)R⁹, —NR⁷C(O)—OR⁹, —NR⁷OR⁹, —OCX₃, —OCHX₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; R⁷, R⁸, R⁹, and R¹⁰ areindependently hydrogen, halogen, —CF₃, —CN, —OH, —NH₂, —COOH, —CONH₂,—NO₂, —SH, —SO₂Cl, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC═(O)NHNH₂,—NHC═(O)NH₂, —NHSO₂H, —NHC═(O)H, —NHC(O)—OH, —NHOH, —OCF₃, —OCHF₂,substituted or unsubstituted alkyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted heterocycloalkyl, substituted or unsubstituted aryl, orsubstituted or unsubstituted heteroaryl; m and v are independently 1 or2; n is independently an integer from 0 to 4; and each X isindependently —Cl, —Br, —I, or —F.
 10. The K-Ras protein of claim 9,wherein R¹ is R³-substituted or unsubstituted aryl; R³ is independentlyoxo, halogen, —OR¹⁰, substituted or unsubstituted aryl, or substitutedor unsubstituted heteroaryl; and R¹⁰ is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, or substituted or unsubstitutedalkyl.